Gene

KWMTBOMO16282

Pre Gene Modal

BGIBMGA002957

Annotation

PREDICTED:_zinc_finger_CCHC_domain-containing_protein_13-like_[Bombyx_mori]

Location

Bomo_Chr28(-):3777320-3777891      View in EpiBrowser

Full name

Gag polyprotein      

Alternative Name

Pr55Gag

Location in the cell

Nuclear   Reliability : 2.112

CDS

ATGCGACGTGTCACCCAAACCGATGCGGAGGTTATTCCAACGTTCCGGCCGGATGAAAAATCTAGCAACGTCAAGGGATGGCTGCACAAGATCGACCAGTTGGATCACGTATATGGATGGGACAACAAAGACTGCCAGTTCATCATGCAGATATGTCTTCGTGGGTCGGCTAGGGATTGTGCGATACACCACCGCAACTATACTACACATCCGCGAATGGCTACCACATGGAGAAGAGAAGGTGCTGTTACTCCAGTTGCAAGAGGGACCGACTTTCAACCAAAGAAATGTTACGCCTGCCGAAGAGAAGGTCATGAAACAAAGAACTGCAAAGAGCCGCGCTGCGAGGTGTGCCATCGCCCGGGACACACGTCGGTCAGCTGA

Protein

MRRVTQTDAEVIPTFRPDEKSSNVKGWLHKIDQLDHVYGWDNKDCQFIMQICLRGSARDCAIHHRNYTTHPRMATTWRREGAVTPVARGTDFQPKKCYACRREGHETKNCKEPRCEVCHRPGHTSVS

Description

Gag polyprotein: Mediates, with Gag-Pol polyprotein, the essential events in virion assembly, including binding the plasma membrane, making the protein-protein interactions necessary to create spherical particles, recruiting the viral Env proteins, and packaging the genomic RNA via direct interactions with the RNA packaging sequence (Psi).
Matrix protein p17: Targets the polyprotein to the plasma membrane via a multipartite membrane-binding signal, that includes its myristoylated N-terminus (By similarity). Matrix protein is part of the pre-integration complex. Implicated in the release from host cell mediated by Vpu. Binds to RNA (By similarity).
Capsid protein p24: Forms the conical core that encapsulates the genomic RNA-nucleocapsid complex in the virion. Most core are conical, with only 7% tubular. The core is constituted by capsid protein hexamer subunits. The core is disassembled soon after virion entry (By similarity). Host restriction factors such as TRIM5-alpha or TRIMCyp bind retroviral capsids and cause premature capsid disassembly, leading to blocks in reverse transcription. Capsid restriction by TRIM5 is one of the factors which restricts HIV-1 to the human species. Host PIN1 apparently facilitates the virion uncoating (By similarity). On the other hand, interactions with PDZD8 or CYPA stabilize the capsid (By similarity).
Nucleocapsid protein p7: Encapsulates and protects viral dimeric unspliced genomic RNA (gRNA). Binds these RNAs through its zinc fingers. Acts as a nucleic acid chaperone which is involved in rearangement of nucleic acid secondary structure during gRNA retrotranscription. Also facilitates template switch leading to recombination. As part of the polyprotein, participates in gRNA dimerization, packaging, tRNA incorporation and virion assembly.
p6-gag: Plays a role in budding of the assembled particle by interacting with the host class E VPS proteins TSG101 and PDCD6IP/AIP1.

Catalytic Activity

3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid.
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1)

Cofactor

Mg(2+)

Subunit

Gag polyprotein: Homotrimer; further assembles as hexamers of trimers. Oligomerization possibly creates a central hole into which the cytoplasmic tail of the gp41 envelope protein may be inserted.Gag polyprotein: Interacts with host TRIM22; this interaction seems to disrupt proper trafficking of Gag polyprotein and may interfere with budding. Gag polyprotein: Interacts with host PDZD8. Matrix protein p17: Homotrimer; further assembles as hexamers of trimers. Matrix protein p17: Interacts with gp41 (via C-terminus). Matrix protein p17: Interacts with host CALM1; this interaction induces a conformational change in the Matrix protein, triggering exposure of the myristate group. Matrix protein p17: Interacts with host AP3D1; this interaction allows the polyprotein trafficking to multivesicular bodies during virus assembly. Matrix protein p17: Part of the pre-integration complex (PIC) which is composed of viral genome, matrix protein, Vpr and integrase. Capsid protein p24: Homodimer; the homodimer further multimerizes as homohexamers or homopentamers. Capsid protein p24: Interacts with human PPIA/CYPA. Capsid protein p24: Interacts with human NUP153. Capsid protein p24: Interacts with host PDZD8; this interaction stabilizes the capsid. Capsid protein p24: Interacts with monkey TRIM5; this interaction destabilizes the capsid. p6-gag interacts with Vpr; this interaction allows Vpr incorporation into the virion. p6-gag interacts with host TSG101. p6-gag interacts with host PDCD6IP/AIP1.

Miscellaneous

HIV-1 lineages are divided in three main groups, M (for Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast majority of strains found worldwide belong to the group M. Group O seems to be endemic to and largely confined to Cameroon and neighboring countries in West Central Africa, where these viruses represent a small minority of HIV-1 strains. The group N is represented by a limited number of isolates from Cameroonian persons. The group M is further subdivided in 9 clades or subtypes (A to D, F to H, J and K).

Similarity

Belongs to the primate lentivirus group gag polyprotein family.

Keywords

3D-structure   AIDS   Capsid protein   Host cell membrane   Host cytoplasm   Host endosome   Host membrane   Host nucleus   Host-virus interaction   Lipoprotein   Membrane   Metal-binding   Methylation   Myristate   Phosphoprotein   Repeat   Ribosomal frameshifting   RNA-binding   Viral budding   Viral budding via the host ESCRT complexes   Viral nucleoprotein   Viral release from host cell   Virion   Zinc   Zinc-finger  

Feature

chain  Gag polyprotein
peptide  Spacer peptide 1

Uniprot

H9J0C1   H9JKH1   A0A139W9F7   Q87621   V9QIN8   Q79351   + More
Q8ADE9   Q8ADV1   D3X833   A0A0H3Y7D9   A0A0H3Y865   A0A386QZH4   C9DWL7   Q8AC28   Q7SPP5   Q9J6W5   A9Y691   C9DX50   Q8AC47   A0A059WHM7   B6DQT6   F5CTF0   D3X851   Q6JFX9   A0A0H3Y6T0   Q8ADN7   Q8AD77   Q6X6X8   U6BH18   Q1KWI1   A0A0H3Y9B5   B2Z220   Q5U6V8   A0A1I9WBM0   Q7ZNK7   L7TH34   W5VSJ1   Q6H1N0   W5VTT7   Q5U6W1   Q8AC19   A0A386QZJ2   Q5Q9E0   D2CJU2   A0A386QZS4   B6DQP6   A0A1B3YUV4   Q9J6V9   C7ASC4   C9DX63   C9DX69   A0A1B3YUZ9   A0A386QZI7   D8X027   C9DWB8   Q8AC39   P12495   A0A1B3YUZ5   A0A2L1KWD2   A0A1B3YV34   C7ARK4   I6RC51   Q5Q9E1   Q6UEW7  

Pubmed

19121390    18362917    19820115    8661445    8363755    12487816    + More
26041893    22039546    10590125    18544023    24926043    15186532    15320994    16701907    15767414    23123038    15585105    27403940    20567513    12873766    29389981    22412369    15186527   

EMBL

BABH01010590    BABH01024735    BABH01024736    KQ972323    KXZ75922.1    U42720    + More
AAB47723.1    KF859747    AHC30187.1    L11769    AAA44689.1    AF484513    AAN73754.1    AF484494    AAN73583.1    GU245717    ADD31665.1    KR860760    AKN05007.1    KR860711    AKN04909.1    MH971628    AYE55483.1    GQ431214    ACV94279.1    AAN73755.1    AJ519489    CAD59562.1    AF184496    AAF28628.1    EU110090    ABW86715.1    GQ431487    ACV94462.1    AAN73584.1    KJ671537    AIA09009.1    FJ155131    ACI05374.1    JF804766    AEE41037.1    GU245738    ADD31683.1    AY492788    AAT06727.1    KR860645    AKN04777.1    AF484502    AAN73655.1    AF484522    AAN73835.1    AY253304    AAQ98120.1    KF716490    AHA33898.1    DQ396380    ABF00749.1    KR860891    AKN05269.1    EU581828    ACD02839.1    AY803372    AAV50143.1    KU921966    APA29369.1    AJ488927    CAD44561.1    CAD58643.1    JX202935    AGC32287.1    KF823032    AHH85799.1    AY455785    AAS59240.1    KF823025    AHH85792.1    AY803367    AAV50140.1    AAN73836.1    MH971621    AYE55476.1    AY772967    AAV85026.1    EF513541    ABU48907.1    MH971715    AYE55570.1    FJ155088    ACI05334.1    KX302424    AOH69338.1    AF184502    AAF28634.1    FJ606395    ACU31735.1    GQ431503    ACV94475.1    GQ431509    ACV94481.1    KX302466    AOH69372.1    MH971638    AYE55493.1    GU458744    ADJ58364.1    GQ430961    ACV94180.1    AAN73656.1    M22639    KX302467    AOH69374.1    MF109468    AVE26833.1    KX302509    AOH69406.1    FJ606125    ACU31465.1    JQ403079    AFM44393.1    AY772965    AAV85025.1    AY371157    AAR22188.1   

Proteomes

UP000005204    UP000007266    UP000246900    UP000133248    UP000152580    UP000124046    + More
UP000181125    UP000102958    UP000247135    UP000138984    UP000115917    UP000126113    UP000118657    UP000123120    UP000140049    UP000133307    UP000100892    UP000174451    UP000160695   

PRIDE

H9J0C1    H9JKH1    P12495   

Pfam

PF17919   RT_RNaseH_2        + More
PF14291   DUF4371
PF17921   Integrase_H2C2
PF00665   rve
PF00078   RVT_1
PF00540   Gag_p17
PF00607   Gag_p24
PF00098   zf-CCHC
PF08705   Gag_p6
PF00552   IN_DBD_C
PF06815   RVT_connect
PF06817   RVT_thumb
PF00077   RVP
PF02022   Integrase_Zn
PF00075   RNase_H

Interpro

IPR036875   Znf_CCHC_sf        + More
IPR001878   Znf_CCHC       
IPR025398   DUF4371       
IPR041577   RT_RNaseH_2       
IPR001584   Integrase_cat-core       
IPR012337   RNaseH-like_sf       
IPR021109   Peptidase_aspartic_dom_sf       
IPR000477   RT_dom       
IPR036397   RNaseH_sf       
IPR041588   Integrase_H2C2       
IPR010999   Retrovr_matrix       
IPR000071   Lentvrl_matrix_N       
IPR000721   Gag_p24       
IPR008919   Retrov_capsid_N       
IPR008916   Retrov_capsid_C       
IPR012344   Matrix_HIV/RSV_N       
IPR014817   Gag_p6       
IPR010659   RVT_connect       
IPR036862   Integrase_C_dom_sf_retrovir       
IPR001969   Aspartic_peptidase_AS       
IPR003308   Integrase_Zn-bd_dom_N       
IPR001995   Peptidase_A2_cat       
IPR010661   RVT_thumb       
IPR002156   RNaseH_domain       
IPR018061   Retropepsins       
IPR001037   Integrase_C_retrovir       
IPR034170   Retropepsin-like_cat_dom       
IPR017856   Integrase-like_N       

SUPFAM

SSF57756   SSF57756        + More
SSF53098   SSF53098       
SSF47836   SSF47836       
SSF47943   SSF47943       
SSF50630   SSF50630       
SSF46919   SSF46919       
SSF50122   SSF50122       

Gene 3D

2.40.70.10     3.30.420.10     1.10.1200.30     1.10.150.90     1.10.375.10     1.10.10.200     2.30.30.10    

CDD

cd05482  HIV_retropepsin_like

ProteinModelPortal

H9J0C1   H9JKH1   A0A139W9F7   Q87621   V9QIN8   Q79351   + More
Q8ADE9   Q8ADV1   D3X833   A0A0H3Y7D9   A0A0H3Y865   A0A386QZH4   C9DWL7   Q8AC28   Q7SPP5   Q9J6W5   A9Y691   C9DX50   Q8AC47   A0A059WHM7   B6DQT6   F5CTF0   D3X851   Q6JFX9   A0A0H3Y6T0   Q8ADN7   Q8AD77   Q6X6X8   U6BH18   Q1KWI1   A0A0H3Y9B5   B2Z220   Q5U6V8   A0A1I9WBM0   Q7ZNK7   L7TH34   W5VSJ1   Q6H1N0   W5VTT7   Q5U6W1   Q8AC19   A0A386QZJ2   Q5Q9E0   D2CJU2   A0A386QZS4   B6DQP6   A0A1B3YUV4   Q9J6V9   C7ASC4   C9DX63   C9DX69   A0A1B3YUZ9   A0A386QZI7   D8X027   C9DWB8   Q8AC39   P12495   A0A1B3YUZ5   A0A2L1KWD2   A0A1B3YV34   C7ARK4   I6RC51   Q5Q9E1   Q6UEW7  

PDB

5O2U     E-value=0.013994,     Score=83

KEGG

101744763    no KO assigned | (RefSeq) zinc finger CCHC domain-containing protein 13-like

GO

GO:0008270   GO:0003676   GO:0015074   GO:0005634   GO:0039702   GO:0030430   GO:0003723   GO:0019013   GO:0042025   GO:0005198   GO:0016032   GO:0004533   GO:0039657   GO:0046718   GO:0004190   GO:0006310   GO:0003964   GO:0016020   GO:0075732   GO:0020002   GO:0003677   GO:0003887   GO:0044826   GO:0075713   GO:0004523   GO:0055036   GO:0072494   GO:0007608   GO:0005515   GO:0005839   GO:0051603   GO:0046835   GO:0006281   GO:0006259  

Subcellular location

Virion  
Host nucleus  
Host cytoplasm  
Host cell membrane  
Host endosome   These locations are probably linked to virus assembly sites. The main location is the cell membrane, but under some circumstances, late endosomal compartments can serve as productive sites for virion assembly.   With evidence from 6 publications.
Host multivesicular body   These locations are probably linked to virus assembly sites. The main location is the cell membrane, but under some circumstances, late endosomal compartments can serve as productive sites for virion assembly.   With evidence from 6 publications.
Virion membrane  

Length:

127

Number of predicted TMHs:

0

Exp number of AAs in TMHs:

0

Exp number, first 60 AAs:

0

Total prob of N-in:

0.61470

inside

1  -  127

 

 

Pi

334.83415

Theta

176.658444

Tajima's D

2.816878

CLR

0

CSRT

0.969201539923004

Interpretation

Uncertain