[English] 日本語
Yorodumi
- PDB-4wym: Structural basis of HIV-1 capsid recognition by CPSF6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wym
TitleStructural basis of HIV-1 capsid recognition by CPSF6
Components
  • Capsid protein p24
  • ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
KeywordsVIRAL PROTEIN / CAPSID PROTEIN / HEXAMER / ENGINEERED DISULFIDE BONDS / CPSF6 / viral restriction
Function / homology
Function and homology information


exon-exon junction complex binding / : / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / paraspeckles ...exon-exon junction complex binding / : / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / paraspeckles / mRNA 3'-end processing / mRNA 3'-end processing / Signaling by cytosolic FGFR1 fusion mutants / RNA Polymerase II Transcription Termination / protein heterotetramerization / viral budding via host ESCRT complex / ribosomal large subunit binding / Processing of Capped Intron-Containing Pre-mRNA / localization / Signaling by FGFR1 in disease / protein tetramerization / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / mRNA processing / ISG15 antiviral mechanism / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / nuclear speck / ribonucleoprotein complex / symbiont entry into host cell / mRNA binding / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / cytoplasm
Similarity search - Function
Cleavage and polyadenylation specificity factor subunit 6 / CPSF6/7 family / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / RNA recognition motif ...Cleavage and polyadenylation specificity factor subunit 6 / CPSF6/7 family / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Reverse transcriptase connection / Reverse transcriptase connection domain / RNA-binding domain superfamily / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Gag polyprotein / Gag-Pol polyprotein / Cleavage and polyadenylation specificity factor subunit 6
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsBattacharya, A. / Taylor, A.B. / Hart, P.J. / Ivanov, D.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis of HIV-1 capsid recognition by PF74 and CPSF6.
Authors: Bhattacharya, A. / Alam, S.L. / Fricke, T. / Zadrozny, K. / Sedzicki, J. / Taylor, A.B. / Demeler, B. / Pornillos, O. / Ganser-Pornillos, B.K. / Diaz-Griffero, F. / Ivanov, D.N. / Yeager, M.
History
DepositionNov 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein p24
B: Capsid protein p24
C: Capsid protein p24
D: Capsid protein p24
E: Capsid protein p24
F: Capsid protein p24
G: Capsid protein p24
H: Capsid protein p24
I: Capsid protein p24
J: Capsid protein p24
K: Capsid protein p24
L: Capsid protein p24
M: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
N: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
O: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
P: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
Q: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
R: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
S: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
T: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
U: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
V: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
W: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6


Theoretical massNumber of molelcules
Total (without water)324,33423
Polymers324,33423
Non-polymers00
Water00
1
A: Capsid protein p24
B: Capsid protein p24
C: Capsid protein p24
D: Capsid protein p24
E: Capsid protein p24
F: Capsid protein p24
M: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
N: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
O: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
P: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
Q: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
R: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6


Theoretical massNumber of molelcules
Total (without water)163,02112
Polymers163,02112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23970 Å2
ΔGint-158 kcal/mol
Surface area61850 Å2
MethodPISA
2
G: Capsid protein p24
H: Capsid protein p24
I: Capsid protein p24
J: Capsid protein p24
K: Capsid protein p24
L: Capsid protein p24
S: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
T: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
U: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
V: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
W: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6


Theoretical massNumber of molelcules
Total (without water)161,31211
Polymers161,31211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21960 Å2
ΔGint-151 kcal/mol
Surface area61810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.790, 136.030, 207.257
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Capsid protein p24 / Pr55Gag


Mass: 25461.271 Da / Num. of mol.: 12 / Mutation: A14C, E45C, W184A, M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Strain: isolate NY5 / Gene: gag / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12497, UniProt: P12493*PLUS
#2: Protein/peptide
ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6 / Cleavage and polyadenylation specificity factor 68 kDa subunit / CPSF 68 kDa subunit / Pre-mRNA ...Cleavage and polyadenylation specificity factor 68 kDa subunit / CPSF 68 kDa subunit / Pre-mRNA cleavage factor Im 68 kDa subunit / Protein HPBRII-4/7


Mass: 1708.952 Da / Num. of mol.: 11 / Fragment: UNP RESIDUES 313-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPSF6, CFIM68 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q16630

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M sodium formate, ammonium acetate, tri-sodium citrate, sodium/potassium tartrate, sodium oxamate; 0.1 M sodium HEPES, MOPS; 30% glycerol, PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→48.47 Å / Num. obs: 117525 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 62.65 Å2 / Rsym value: 0.065 / Net I/σ(I): 20.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.863 / Mean I/σ(I) obs: 2.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3H4E

3h4e


Resolution: 2.6→48.468 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 28.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2592 2005 1.71 %random
Rwork0.2187 ---
obs0.2194 117427 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.97 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20912 0 0 0 20912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00321406
X-RAY DIFFRACTIONf_angle_d0.56429062
X-RAY DIFFRACTIONf_dihedral_angle_d11.428132
X-RAY DIFFRACTIONf_chiral_restr0.0233250
X-RAY DIFFRACTIONf_plane_restr0.0043800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6650.35281440.2958192X-RAY DIFFRACTION100
2.665-2.73710.33981430.28938141X-RAY DIFFRACTION100
2.7371-2.81760.35211400.28058166X-RAY DIFFRACTION100
2.8176-2.90850.32451400.28738186X-RAY DIFFRACTION100
2.9085-3.01250.34461390.27828137X-RAY DIFFRACTION100
3.0125-3.13310.29891450.2748210X-RAY DIFFRACTION100
3.1331-3.27560.26071420.26478151X-RAY DIFFRACTION100
3.2756-3.44830.31211400.25428218X-RAY DIFFRACTION100
3.4483-3.66430.28971460.24048231X-RAY DIFFRACTION100
3.6643-3.94710.23281410.2198219X-RAY DIFFRACTION100
3.9471-4.34410.23851450.19658298X-RAY DIFFRACTION100
4.3441-4.97210.22331470.17678266X-RAY DIFFRACTION100
4.9721-6.26220.24361450.21288361X-RAY DIFFRACTION100
6.2622-48.47640.22311480.17488646X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more