[English] 日本語
Yorodumi
- PDB-4u0c: Hexameric HIV-1 CA in complex with Nup153 peptide, P6 crystal form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4u0c
TitleHexameric HIV-1 CA in complex with Nup153 peptide, P6 crystal form
Components
  • Capsid protein p24
  • Nuclear pore complex protein Nup153
KeywordsVIRAL PROTEIN / Capsid / Nuclear Pore / FG repeat
Function / homology
Function and homology information


negative regulation of RNA export from nucleus / nuclear pore complex assembly / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA ...negative regulation of RNA export from nucleus / nuclear pore complex assembly / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / nuclear localization sequence binding / structural constituent of nuclear pore / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / viral budding via host ESCRT complex / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / nuclear pore / SUMOylation of DNA damage response and repair proteins / protein-membrane adaptor activity / nuclear periphery / SUMOylation of chromatin organization proteins / HCMV Late Events / molecular condensate scaffold activity / Transcriptional regulation by small RNAs / host multivesicular body / ISG15 antiviral mechanism / viral penetration into host nucleus / protein import into nucleus / HCMV Early Events / nuclear envelope / host cell / viral nucleocapsid / snRNP Assembly / nuclear membrane / amyloid fibril formation / viral translational frameshifting / symbiont entry into host cell / nucleolus / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / membrane / cytosol
Similarity search - Function
Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Zinc finger domain / Gag protein p6 ...Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Zinc finger domain / Gag protein p6 / Gag protein p6 / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Gag polyprotein / Nuclear pore complex protein Nup153
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 Å
AuthorsPrice, A.J. / Jacques, D.A. / James, L.C.
CitationJournal: Plos Pathog. / Year: 2014
Title: Host Cofactors and Pharmacologic Ligands Share an Essential Interface in HIV-1 Capsid That Is Lost upon Disassembly.
Authors: Price, A.J. / Jacques, D.A. / McEwan, W.A. / Fletcher, A.J. / Essig, S. / Chin, J.W. / Halambage, U.D. / Aiken, C. / James, L.C.
History
DepositionJul 11, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein p24
B: Nuclear pore complex protein Nup153


Theoretical massNumber of molelcules
Total (without water)27,1492
Polymers27,1492
Non-polymers00
Water3,603200
1
A: Capsid protein p24
B: Nuclear pore complex protein Nup153
x 6


Theoretical massNumber of molelcules
Total (without water)162,89412
Polymers162,89412
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
crystal symmetry operation4_575-x,-y+2,z1
crystal symmetry operation5_455y-1,-x+y,z1
crystal symmetry operation6_665x-y+1,x+1,z1
Buried area21320 Å2
ΔGint-167 kcal/mol
Surface area60980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.469, 91.469, 57.001
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Detailsbiological unit is the same as asym.

-
Components

#1: Protein Capsid protein p24 / Pr55Gag


Mass: 25461.271 Da / Num. of mol.: 1 / Mutation: yes
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 BL21(DE3) (bacteria) / References: UniProt: P12493
#2: Protein/peptide Nuclear pore complex protein Nup153 / 153 kDa nucleoporin / Nucleoporin Nup153


Mass: 1687.721 Da / Num. of mol.: 1 / Fragment: UNP residues 1407-1423 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49790
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 30% v/v PEG 400, 0.1 M CHES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.77→35.67 Å / Num. obs: 24947 / % possible obs: 95.1 % / Redundancy: 3.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.066 / Net I/σ(I): 7.3 / Num. measured all: 79253 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.77-1.813.20.9421.6457314110.3920.58195.8
9.05-35.6740.03321.47451880.9990.01989.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Aimless0.2.18data scaling
MOSFLMdata reduction
PDB_EXTRACT3.14data extraction
PHASERphasing
REFMAC5.8.0049refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H47

3h47


Resolution: 1.77→35.67 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2042 / WRfactor Rwork: 0.1857 / FOM work R set: 0.8272 / SU B: 2.793 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1212 / SU Rfree: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 1200 4.8 %RANDOM
Rwork0.1913 23742 --
obs0.1923 24942 94.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.61 Å2 / Biso mean: 24.339 Å2 / Biso min: 10.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å20 Å2
2---0.2 Å20 Å2
3---0.66 Å2
Refinement stepCycle: final / Resolution: 1.77→35.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 0 200 1872
Biso mean---33.77 -
Num. residues----219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191751
X-RAY DIFFRACTIONr_bond_other_d0.0010.021667
X-RAY DIFFRACTIONr_angle_refined_deg0.8781.9592388
X-RAY DIFFRACTIONr_angle_other_deg0.7283.0013837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2695226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39224.52173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.90915292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0021511
X-RAY DIFFRACTIONr_chiral_restr0.0510.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211985
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02382
X-RAY DIFFRACTIONr_mcbond_it2.0093.008889
X-RAY DIFFRACTIONr_mcbond_other2.0043.007888
X-RAY DIFFRACTIONr_mcangle_it3.0945.0261108
LS refinement shellResolution: 1.774→1.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 89 -
Rwork0.289 1742 -
all-1831 -
obs--95.07 %

+
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://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