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Table 2 Cellular Proteins in HIV-1 cores a

From: Virus-producing cells determine the host protein profiles of HIV-1 virion cores

Locationb

Gene Namec

Accession Numberd

Protein Namee

Contained in cores produced by:

    

SupT1

Act. THP1

N-Act. THP1

DNA Binding: Chromatin Organization, Replication, Topoisomerases

N,C

RUVBL1

4506753

TATA binding protein interacting protein 49 kDa

✓

✓

✓

M,C,N

MCM5

1232079

Minichromosome maintenance complex component 5

✓

✓

✓

N

RCC2

11360295

Regulator of chromosome condensation protein 2

✓

✓

 

N,C

RUVBL2

5730023

TBP-interacting protein, 48-KD

✓

 

✓

N

TOP2B

288565

DNA topoisomerase II

✓

  

N,C

SSRP1

4507241

Structure specific recognition protein 1

✓

  

N

H2AFY

32492946

H2A histone family, member Y

✓

  

N,C

ERVK-6

3600071

Reverse transcriptase encoded by human endogenous HERV-K retrovirus

✓

  

N,C

MCM7

2134885

Replication licensing factor MCM7

  

✓

N,M

TEP1

1848277

telomerase-associated protein 1; TP-1

  

✓

N

HIST1H1B

4885381

H1 histone family, member 5; H1b

  

✓

N

HIST1H1C

4885375

H1 histone family, member 2; H1d

  

✓

Number of Proteins per Cell Type:

6

3

4

DNA Damage Repair

N

XRCC5

35038

Nuclear factor IV - KU80, ATP-dependant DNA helicase II

✓

✓

✓

N

PRKDC

1362789

DNA-activated protein kinase

 

✓

✓

N

DDB1

12643730

DNA damage binding protein 1

 

✓

 

Number of Proteins per Cell Type:

1

3

2

DNA Binding: Transcription Regulation

N

POLR2B

23270691

Polymerase (RNA) II (DNA directed) polypeptide B

  

✓

N

RHOX11

27715523

Similar to Paired-like homeobox protein OTEX

✓

  

Number of Proteins per Cell Type:

1

0

1

RNA Binding: Structure Organization, Modification, Transport, Splicing

N

UPF1

1575536

Regulator of nonsense transcript stability

✓

✓

✓

N

DHX9

3915658

ATP-dependent RNA helicase A - DEAD box protein 9

✓

✓

✓

N

EFTUD2

24474791

Small nuclear ribonucleoprotein component

✓

✓

✓

N

SNRNP200

14043179

Helicase hBrr2 200 kDa

✓

✓

✓

N

HNRNPM

14141154

Heterogeneous nuclear ribonucleoprotein M isoform b

✓

✓

 

N,C

EIF3A

32449796

Eukaryotic translation initiation factor 3, subunit A

✓

✓

 

N,C

PABPC1

29743688

Poly(A) binding protein, cytoplasmic 1

✓

✓

 

N

PRPF8

17999537

U5 snRNP-specific protein

✓

 

✓

N,C

HNRNPH1

5031753

Heterogeneous nuclear ribonucleoprotein H1

✓

 

✓

N

PDCD7

4416183

ES18 - U12-type spliceosome component

✓

 

✓

N,C

FLII

2135121

Flightless-I homolog

✓

 

✓

C

DDX3X

13514813

Helicase like protein 2 - DEAD/H box polypeptide 3

✓

  

N,C,Mit

DDX17

5453840

RNA-dependent helicase p72 - DEAD box polypeptide 17 isoform 1

✓

  

N

RENT1

1575536

Rregulator of nonsense transcript stability

✓

  

N,C

SYNCRIP

26454828

Synaptotagmin-binding, cytoplasmic RNA-interacting protein

✓

  

N,C

PABP2

12229876

Polyadenylate-binding protein 2

✓

  

N,C

HNRNPR

13629286

Heterogeneous nuclear ribonucleoprotein R

✓

  

N

SNRNP200

14043179

Small nuclear ribonucleoprotein 200 kDa (U5)

✓

  

C

ACO1

9802308

Iron regulatory protein 1

✓

  

C,M

FHL1

6942193

Four and a half LIM domains 1 protein isoform C

✓

  

N

PCBP1

444021

Poly(rC) binding protein 1

✓

  

N,C

HNRNPF

16876910

Heterogeneous nuclear ribonucleoprotein F

✓

  

N,C

SRSF3

4506901

Splicing factor, arginine/serine-rich 3

✓

  

N

RALY

27689091

Autoantigenic RNA binding protein

 

✓

 

N

DDX21

11890755

RNA helicase II/Gu protein - DEAD box polypeptide 21

 

✓

 

N,C,Mit

RTCD1

4506589

RNA 3'-terminal phosphate cyclase

 

✓

 

N,C

HNRNPA1

30157273

Heterogeneous nuclear ribonucleoprotein A1

 

✓

 

V,N,C

EIF5A2

9966867

Eukaryotic translation initiation factor 5A2; eIF-5A2 protein

 

✓

 

N,C

SNUPN

6730226

D3b subcomplex of human core snRNP domain

  

✓

Number of Proteins per Cell Type:

24

11

9

Cytoskeleton

C

MYH10

1346640

Cellular myosin type B, heavy chain

✓

✓

✓

C

MYH9

29436380

Cellular myosin, heavy polypeptide 9

✓

✓

✓

C

TUBA1A

135395

Tubulin α 1

✓

✓

✓

C

TUBA1C

1438930

Tubulin α 6

✓

✓

✓

C

TUBB

1280489

Tubulin β 5

✓

✓

✓

C

TUBB3

1204535

Tubulin β 3

✓

✓

✓

C

ACTBL2

2973662

β Actin

✓

✓

✓

C

TUBB4

2748197

β Tubulin 4Q

✓

✓

 

C

TUBB1

13562114

Tubulin β 1

✓

✓

✓

C

TEKT1

16753231

Tektin 1

✓

  

C

DYNC1H1

30581065

Dynein Heavy Chain, cytosolic

 

✓

✓

C

MYO1F

1924940

Myosin-IF

 

✓

✓

N,M

MYO1G

14269502

Unconventional myosin IG valine form

 

✓

 

C,M

TUBG1

31543831

Tubulin γ 1

  

✓

C

TPM2

6573280

Tropomyosin 2 (β)

  

✓

Number of Proteins per Cell Type:

10

11

12

Cytoskeleton Regulation

C

HSPB1

662841

Heat shock protein 27

✓

✓

✓

M,N

MSN

14625824

Moesin

✓

✓

✓

C

CORO1A

5902134

Coronin, actin binding protein, 1A

✓

✓

✓

M,C,V

CNP

180687

2',3'-cyclic-nucleotide 3'-phosphodiesterase; CNPase

✓

✓

 

N,C

FLII

2135121

Flightless-I homolog

✓

 

✓

M,C

TTLL10

27663488

Tubulin tyrosine ligase-like family, member 10

✓

  

C

ACTR2

27500905

Human ARP2 actin-related protein 2 homolog (yeast)

✓

  

C,N

8-SEP

12654963

SEPT11 - Septin filament-forming cytoskeletal GTPase family member 11

✓

  

N,C

PFN1

3891601

Human platelet profilin chain A

✓

  

C,N

ACTR3

5031573

Human ARP3 actin-related protein 3 homolog (yeast)

 

✓

 

C

DNAJA1

219588

DnaJ (Hsp40) homolog, subfamily A, member 1

 

✓

 

C

RHOA

12654251

RAS homolog gene family, member A

 

✓

 
 

ARPC4-TTLL3

10436409

Actin related protein 2/3 complex, subunit 4-tubulin tyrosine ligase-like family, member 3 read-through fusion protein

 

✓

 

C

ARPC4

15214920

Actin related protein 2/3 complex, subunit 4

 

✓

 

C

RAC2

4506381

RAS-related C3 botulinum toxin substrate 2

 

✓

 

M,V,C

TLN1

6739602

Talin

  

✓

M,C

FLNA

1203969

Filamin

  

✓

M

SPG8

20070788

Strumpellin

  

✓

C

NCKAP1L

32425702

HEM1 protein

  

✓

C

TBCD

13111855

Tubulin folding cofactor D

  

✓

M,C

CAP1

29739285

Human adenylyl cyclase-associated CAP protein homolog 1 (S. cerevisiae, S. pombe)

  

✓

Number of Proteins per Cell Type:

9

10

10

Cell Signaling

N,C

GNB2L1

5174447

Guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1

✓

✓

✓

 

MYADM

27730943

Myeloid-associated differentiation marker

 

✓

✓

C,V

PTPRC

10999057

Protein tyrosine phosphatase

 

✓

✓

M

SEMA7A

3551779

Semaphorin L

✓

  

M,C

PKN1

1085381

Serine/threonine protein kinase

✓

  

C,M

MMP14

1705985

Matrix metalloproteinase 14

 

✓

 

C

TIMP3

1304484

Tissue inhibitor of metalloproteinases-3

 

✓

 

Number of Proteins per Cell Type:

3

5

3

Nuclear Import

N,C

TNPO1

27681051

Karyopherin β2; importin β 2; transportin; transportin 1

 

✓

✓

V,N

TNPO3

6912734

Transportin-SR; importin 12; transportin-SR2

✓

  

N,C

KPNB1

19923142

Karyopherin β1; importin 90; importin β-1

  

✓

N

KPNA2

1354365

Karyopherin α2; RAG cohort 1, importin α1

  

✓

Number of Proteins per Cell Type:

1

1

3

Nuclear Export

N

XPO5

12407633

RANBP21/exportin 5

✓

 

✓

N,C

XPOT

17367977

Exportin T (tRNA exportin)

✓

 

✓

Number of Proteins per Cell Type:

2

0

2

Apoptosis

C

HP95

13375569

Programmed cell death 6 interacting protein

✓

✓

✓

Number of Proteins per Cell Type:

1

1

1

Extracellular Signaling

V,C,M

PTPRC

10999057

Protein tyrosine phosphatase, receptor type, C

 

✓

 

C

AIMP1

27065983

Aminoacyl tRNA synthetase complex-interacting multifunctional protein 1

✓

  

M

CLEC1A

30159086

C-type lectin domain family 1, member A

✓

  

Number of Proteins per Cell Type:

2

1

0

Intracellular Transport

C,M

CLTC

30353925

Clathrin, heavy chain (Hc)

✓

✓

✓

M,C

RAB8A

234746

RAB8A, member RAS oncogene family

✓

✓

✓

M

CPNE1

4503013

Copine I

 

✓

✓

C,N

TNIP1

1800305

TNFAIP3 interacting protein 1; HIV-1 Nef interacting protein

✓

  

M,N,C

GC

18655422

Vitamin D binding protein

 

✓

 

M,C

AP2B1

33504652

Adaptor-related protein complex 2, β1 subunit

  

✓

Number of Proteins per Cell Type:

3

4

4

RNA Stability Regulation

C,N

RNH1

15029922

Ribonuclease/angiogenin inhibitor 1

✓

  

Number of Proteins per Cell Type:

1

0

0

Nuclear Lamina, intranuclear components

N

LMNB1

15126742

lamin B1

✓

  

N

NCL

21750187

Nucleolin

✓

  

N

DKC1

14602859

Dyskerin; dyskeratosis congenita 1

✓

  

N

RPL3

18606060

Ribosomal protein L3

✓

  

Number of Proteins per Cell Type:

4

0

0

Cell adhesion

M,C

PCDHGA7

14196477

Protocadherin gamma subfamily A, 7

✓

  

M

HABP2

4758502

Hyaluronan binding protein 2

✓

  

Number of Proteins per Cell Type:

2

0

0

Mitochondria

Mit

SLC25A6

113463

Solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6

 

✓

 

Number of Proteins per Cell Type:

0

1

0

Lipid Biosynthesis

C,N

FDFT1

11514495

Farnesyl-diphosphate farnesyltransferase 1

✓

  

M,C

FASN

15779138

Fatty acid synthase

 

✓

 

Number of Proteins per Cell Type:

1

1

0

Transmembrane Ion Transport

N,M

SLC4A10

7513341

Sodium bicarbonate cotransport protein 2

✓

  

C,M

ATP6V0E2

542837

ATPase, H + transporting V0 subunit e2

 

✓

 

Number of Proteins per Cell Type:

1

1

0

Cell-Cell Transport

M,C

ESYT1

7512911

Extended synaptotagmin-like protein 1

 

✓

 

Number of Proteins per Cell Type:

0

1

0

Ribosomal

R

RPL7A

4506661

60 S-L7A

✓

✓

✓

R

RPL18A

11415026

60 S-L18A

✓

✓

✓

R

RPL7A

17456110

60 S-L7

✓

✓

 

R

 

27483402

40 S-S2

✓

✓

 

R

RPL7L1

27498574

60 S-L7Like1

✓

 

✓

R

RPL13

15431295

60 S-L13

✓

 

✓

R

RPL24

4506619

60 S-L24

 

✓

✓

R

RPS8

4506743

40 S-S8

✓

  

Number of Proteins per Cell Type:

7

5

5

Ubiquitin/Proteasome

C,N

UBA1

24485

Ubiquitin-like modifier activating enzyme 1

✓

✓

✓

C

BFAR

27675450

Bifunctional apoptosis regulator

✓

✓

✓

N,C

PSMC3

107855

Proteasome (prosome, macropain) 26 S subunit, ATPase, 3

✓

✓

✓

C

PSMD7

2134660

Proteasome (prosome, macropain) 26 S subunit, non-ATPase, 7

✓

  

M,C

PSMB1

12653473

Proteasome (prosome, macropain) subunit, β type, 1

✓

  

N,C

PSMD11

2150046

Proteasome (prosome, macropain) 26 S subunit, non-ATPase, 11

✓

  

C,N

PAAF1

33150632

Proteasomal ATPase-associated factor 1

 

✓

 

C,N

RPN1

14124942

Ribophorin I

 

✓

 

N,C

PSMD3

16550621

Proteasome (prosome, macropain) 26 S subunit, non-ATPase, 3

 

✓

 

Number of Proteins per Cell Type:

6

6

3

Metabolism, Metabolism Regulation

M

PFKP

11321601

Phosphofructokinase, platelet

✓

✓

✓

C,N,M

ACLY

13623199

ATP citrate lyase

 

✓

✓

M,C

PYGL

10120741

Chain A, Human Liver Glycogen Phosphorylase A

 

✓

✓

N,C

GPT

1507680

Glutamic-pyruvate transaminase (alanine aminotransferase)

✓

  

C,M

PKM2

125604

Pyruvate kinase, M2 isozyme

✓

  

C

SLC2A1

3387905

Solute carrier family 2 (facilitated glucose transporter), member 1

✓

  

N,C

TPI1

16877874

Triosephosphate isomerase 1

 

✓

 

Number of Proteins per Cell Type:

4

4

3

Cell Cycle Regulation/Cell Differentiation

N

CCNB3

14719420

Cyclin B3 isoform 3

✓

✓

✓

C

PPP2R1A

21749746

Protein phosphatase 2A, regulatory subunit A, α

✓

 

✓

C,M

RAP1B

12751117

RAP1B, member of RAS oncogene family

 

✓

✓

C,N

PPP2R3B

7019501

Protein phosphatase 2A, regulatory subunit B'', β; PP2A B''

✓

  

N,C

CDK11A

16357490

Cyclin-dependent kinase 11A

✓

  

C

PRDX3

32483377

Peroxiredoxin 3 isoform b

 

✓

 

C

TIMP3

1304484

TIMP metallopeptidase inhibitor 3

 

✓

 

Number of Proteins per Cell Type:

4

4

3

Nucleotide Biosynthesis

C

CAD

18105007

Carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase

✓

  

Number of Proteins per Cell Type:

1

0

0

Amino Acid Biosynthesis

M,C,N

PHGDH

5771521

3-phosphoglycerate dehydrogenase

✓

  

C

ASS1

16950633

Argininosuccinate synthase 1

 

✓

 

C

GCN1L1

2282576

HsGCN1; GCN1 general control of amino-acid synthesis 1-like 1 (human homolog of yeast)

  

✓

Number of Proteins per Cell Type:

1

1

1

Vesicular Transport

C,M

CLTC

30353925

Clathrin

✓

✓

✓

C,M,V

COPA

4758030

Coatomer protein complex, subunit α; alpha coat protein; xenin

✓

✓

✓

V,C

MVP

19913410

Major Vault Protein

✓

✓

✓

C,V

TFRC

4507457

Transferrin receptor (p90, CD71)

✓

✓

✓

C,V

RAB7A

1709999

RAB7A, member RAS oncogene family

✓

✓

✓

C

PDCD6IP

13375569

Programmed cell death 6 interacting protein, HP95, AIP1/ALIX

✓

✓

✓

C

RAB5C

4759020

RAB5C, member RAS oncogene family

 

✓

✓

C,V

EHD4

7212811

EH-domain containing 4

 

✓

 

C

SAR1A

21634445

GTP-binding protein Sara; SAR1 homolog A (S. cerevisiae)

 

✓

 

M,V

ARFRP1

1065361

Chain A, Human Adp-ribosylation factor related protein 1

 

✓

 

V,N

ATP6V0A1

1638835

ATPase, H + transporting, lysosomal V0 subunit a1

 

✓

 

C

RAB11A

4758984

RAB11A, member RAS oncogene family

  

✓

Number of Proteins per Cell Type:

5

10

7

Aminoacyl tRNA synthetases

C,N

IARS

31873336

Isoleucyl-tRNA synthetase

✓

✓

✓

C,N

MARS

15929104

Methionyl-tRNA synthetase

✓

 

✓

C,N

RARS

2118344

Arginyl-tRNA synthetase

✓

  

C,N

GARS

3845409

Glycyl-tRNA synthetase

✓

  

C,Mit

WARS

8439415

Tryptophanyl-tRNA synthetase

✓

  

C,N

DARS

4557513

Aspartyl-tRNA synthetase

 

✓

 

C,N

QARS

11493441

Glutaminyl-tRNA synthetase

 

✓

 

Number of Proteins per Cell Type:

5

3

2

Translation and Translation Regulation

N,C

EIF3A

32449796

Eukaryotic translation initiation factor 3, subunit A

✓

✓

 

C

EEF2

4503483

Eukaryotic translation elongation factor 2; polypeptidyl-tRNA translocase

✓

  

C

CC2D1B

27715655

Coiled-coil and C2 domain containing 1B

✓

  

C

CYFIP1

24307969

Cytoplasmic FMR1 interacting protein 1 (Sra1)

 

✓

 

C

AIMP2

27662300

Aminoacyl tRNA synthetase complex-interacting multifunctional protein 2

 

✓

 

V,N,C

EIF5A2

9966867

Eukaryotic translation initiation factor 5A2; eIF-5A2 protein

 

✓

 

Number of Proteins per Cell Type:

3

4

0

Protein Post-Translation Modification

C,M

PAFAH1B

4505587

Platelet-activating factor acetylhydrolase 1b, catalytic subunit 3

✓

  

N,C

PARP1

130781

Poly [ADP-ribose] polymerase-1

✓

  

C

USP14

4827050

Ubiquitin specific protease 14

✓

  

C,N

SERPINC1

4502261

Serpin peptidase inhibitor, clade C (antithrombin), member 1

✓

  

M,C

LPL

15030193

Lipoprotein lipase

 

✓

 

M,C

NMT1

345862

N-myristoyltransferase 1

 

✓

 

C,M

CPD

21903712

Carboxypeptidase D

 

✓

 

Number of Proteins per Cell Type:

4

3

0

Protein Degradation (non-proteasomal)

M

ANPEP

28678

Alanyl (membrane) aminopeptidase

 

✓

 

Number of Proteins per Cell Type:

0

1

1

Chaperones/Molecular Folding

C

DNAJC13

7513063

DnaJ (Hsp40) homolog, subfamily C, member 13

✓

✓

✓

C

HSP90AB1

20149594

Heat shock protein 90 kDa α (cytosolic), class B member 1

✓

✓

✓

C,N

HSPA8

24234686

Heat shock 70 kDa protein 8

✓

✓

✓

C,M, N

CCT3

2136253

Chaperonin containing t-complex polypeptide 1 (TCP1), subunit 3 (γ); TCP1 ring complex protein TRiC5

✓

✓

✓

C,M

CCT6A

4502643

Chaperonin containing t-complex polypeptide 1 (TCP1), subunit 6A (ζ1)

✓

✓

✓

C,M

CCT6B

22654293

Chaperonin containing t-complex polypeptide 1 (TCP1), subunit ζ2

✓

✓

✓

C

HSPB1

662841

Heat shock 27 kDa protein 1

✓

✓

✓

C

PPIA

2624881

Human Cyclophilin A

✓

✓

✓

N

NAP1L4

5174613

Nucleosome assembly protein 1-like 4; nucleosome assembly protein 2

✓

 

✓

N,M,C

TCP1

13540473

t-complex polypeptide 1 (TCP1)

✓

 

✓

N,C

CCT5

12804225

Chaperonin containing t-complex polypeptide 1 (TCP1), subunit 5 (ϵ)

✓

  

C

P4HB

20070125

Prolyl 4-hydroxylase, β polypeptide

 

✓

 

C

CCT7

5453607

Chaperonin containing t-complex polypeptide 1 (TCP1), subunit η

 

✓

 

C

SERPINH1

123576

Serpin peptidase inhibitor, clade H (heat shock protein 47), member 1

 

✓

 

C

HYOU1

5453832

Oxygen regulated protein 1

 

✓

 

C

CANX

10716563

Calnexin

 

✓

 

Mit

HSPA9

12653415

Heat shock 70 kDa protein 9 (mortalin)

 

✓

 

C,N

CCT4

2559008

Chaperonin containing t-complex polypeptide 1 (TCP1), subunit δ

  

✓

Number of Proteins per Cell Type:

10

13

10

  1. a Cellular proteins were detected in the cores from the virions produced by different types of infected cells. Proteins are listed by functional category and indicated as being within the core from a specific producer type by a check symbol (✓). Bolded proteins were found in viral cores produced by all producer cells.
  2. b The locations of listed proteins are abbreviated as follows: C – Cytoplasmic, N – Nucleus, M – Plasma Membrane, Mit – Mitochondria, R – Endoplasmic Reticulum, V – Vesicles.
  3. c Official Gene Symbol as listed by HGNC.
  4. d Swiss-Prot Protein Accession number.
  5. e Full Protein name as listed in NCBI Protein Database (http://www.ncbi.nlm.nih.gov/protein).