[English] 日本語
Yorodumi
- PDB-5b56: Crystal structure of HIV-1 VPR C-Terminal domain and DIBB-M-Impor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5b56
TitleCrystal structure of HIV-1 VPR C-Terminal domain and DIBB-M-Importin-Alpha2 complex
Components
  • Importin subunit alpha-1
  • Protein Vpr
KeywordsPROTEIN TRANSPORT/VIRAL PROTEIN / ARM REPEAT / ALL ALPHA PROTEIN / NUCLEAR IMPORT / IMPORTIN-BETA / NLS-CARGO / PROTEIN TRANSPORT-VIRAL PROTEIN COMPLEX
Function / homology
Function and homology information


symbiont-mediated arrest of host cell cycle during G2/M transition / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / monoatomic ion transmembrane transport ...symbiont-mediated arrest of host cell cycle during G2/M transition / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / monoatomic ion transmembrane transport / virion component / protein homooligomerization / cytoplasmic stress granule / viral penetration into host nucleus / protein import into nucleus / host cell / DNA-binding transcription factor binding / host extracellular space / postsynaptic density / symbiont entry into host cell / cell cycle / DNA-templated transcription / glutamatergic synapse / host cell nucleus / regulation of DNA-templated transcription / nucleoplasm / nucleus / cytosol
Similarity search - Function
Retroviral VpR/VpX protein / VPR/VPX protein / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. ...Retroviral VpR/VpX protein / VPR/VPX protein / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1 / Protein Vpr
Similarity search - Component
Biological speciesMus musculus (house mouse)
HIV-1 M:B_89.6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMiyatake, H. / Sanjoh, A. / Matusda, G. / Murakami, T. / Murakami, H. / Hagiwara, K. / Yokoyama, M. / Sato, H. / Miyamoto, Y. / Dohmae, N. / Aida, Y.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Molecular Mechanism of HIV-1 Vpr for Binding to Importin-alpha
Authors: Miyatake, H. / Sanjoh, A. / Murakami, T. / Murakami, H. / Matsuda, G. / Hagiwara, K. / Yokoyama, M. / Sato, H. / Miyamoto, Y. / Dohmae, N. / Aida, Y.
History
DepositionApr 25, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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: Importin subunit alpha-1
B: Importin subunit alpha-1
C: Protein Vpr
D: Protein Vpr
E: Protein Vpr
F: Protein Vpr


Theoretical massNumber of molelcules
Total (without water)105,3436
Polymers105,3436
Non-polymers00
Water9,224512
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint22 kcal/mol
Surface area39030 Å2
Unit cell
Length a, b, c (Å)91.021, 81.555, 101.545
Angle α, β, γ (deg.)90.00, 97.78, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Importin subunit alpha-1 / Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit ...Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / RAG cohort protein 1 / SRP1-alpha


Mass: 49886.633 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 70-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#2: Protein/peptide
Protein Vpr / R ORF protein / Viral protein R


Mass: 1392.526 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN, UNP RESIDUES 85-96 / Source method: obtained synthetically / Details: SYNTHETIC PEPTIDE / Source: (synth.) HIV-1 M:B_89.6 (virus) / References: UniProt: Q73369
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 50MM MES, 100MM AMMONIUM SULFATE, 10MM MGCL2, 20-23%(W/V) PEG8000, 5MM DTT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Feb 11, 2009
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.298→31.523 Å / Num. obs: 57284 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 39.93 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 24.7
Reflection shellResolution: 2.3→2.34 Å / % possible all: 51

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.1_1168phasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KND

3knd


Resolution: 2.3→31.52 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0.21 / Phase error: 25.36
RfactorNum. reflection% reflection
Rfree0.226 2906 5.07 %
Rwork0.182 --
obs0.184 57284 87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 71.74 Å2
Refinement stepCycle: LAST / Resolution: 2.3→31.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6951 0 0 512 7463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037063
X-RAY DIFFRACTIONf_angle_d0.7249601
X-RAY DIFFRACTIONf_dihedral_angle_d14.2352610
X-RAY DIFFRACTIONf_chiral_restr0.0281147
X-RAY DIFFRACTIONf_plane_restr0.0031239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2982-2.33590.4092870.34381515X-RAY DIFFRACTION51
2.3359-2.37610.33021210.32361911X-RAY DIFFRACTION66
2.3761-2.41930.33181200.30812100X-RAY DIFFRACTION71
2.4193-2.46590.33641300.30072229X-RAY DIFFRACTION75
2.4659-2.51620.33021120.29392239X-RAY DIFFRACTION76
2.5162-2.57090.32541230.27232327X-RAY DIFFRACTION79
2.5709-2.63070.31711200.25322502X-RAY DIFFRACTION83
2.6307-2.69650.27431280.23722530X-RAY DIFFRACTION86
2.6965-2.76940.28631420.22262584X-RAY DIFFRACTION88
2.7694-2.85080.2791210.21842659X-RAY DIFFRACTION89
2.8508-2.94280.2681460.20442660X-RAY DIFFRACTION90
2.9428-3.0480.23691410.19522744X-RAY DIFFRACTION92
3.048-3.170.25351510.19692845X-RAY DIFFRACTION95
3.17-3.31420.24021450.19432863X-RAY DIFFRACTION96
3.3142-3.48890.221640.18312910X-RAY DIFFRACTION98
3.4889-3.70740.22291570.15922921X-RAY DIFFRACTION98
3.7074-3.99340.19971610.14012899X-RAY DIFFRACTION98
3.9934-4.39490.1481360.13313002X-RAY DIFFRACTION99
4.3949-5.03010.17271590.13772987X-RAY DIFFRACTION99
5.0301-6.33420.22781680.18112962X-RAY DIFFRACTION99
6.3342-43.40640.18671740.15442989X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3210.562-0.49051.44790.95921.14990.0760.4480.1265-0.73550.0048-0.5473-0.13830.92890.00250.7096-0.06420.08760.72670.12120.619368.1292-16.242345.5953
23.8931-2.4870.6370.8217-0.6147-0.0197-0.1173-0.25690.01030.11650.0640.0282-0.063-0.019100.3233-0.0352-0.04990.36490.01260.542538.2426-8.672955.7619
34.2438-0.7699-0.08162.922-0.6422.19540.23670.5257-0.227-0.765-0.04830.20950.4872-0.24970.00060.4564-0.0534-0.03070.4634-0.01370.37294.61510.22136.6654
42.4582-0.358-0.18113.8553-0.4063.99490.17070.2184-0.2129-0.1322-0.003-0.45630.26220.4060.00170.48060.05140.00030.4391-0.03730.34293.8855-20.2957-19.6548
51.0239-0.92190.83742.1497-2.13534.4367-0.2064-0.09290.07640.18940.2366-0.0667-0.3974-0.1731-0.00160.54670.07360.04090.4025-0.03690.383-2.2397-33.835219.7313
60.70850.2641-0.21062.4465-1.01381.9851-0.4752-0.53010.3854-0.0271-0.1735-1.4478-0.88431.5862-0.13771.7336-0.0764-0.15620.9896-0.31031.102612.8747-30.536648.163
70.13820.0854-0.28580.0768-0.24521.0367-0.3716-0.0426-1.4077-0.2659-0.36980.15141.32660.208100.88310.0010.070.5138-0.05690.939717.1867-11.921745.2395
80.19880.01240.16110.4367-0.14660.2383-0.02240.280.7450.55750.0749-0.347-0.9015-0.29760.00911.19370.1004-0.05110.68490.05340.692-0.9276-24.035422.2413
91.57420.30310.2020.2846-0.01150.034-0.00320.12950.4696-0.5145-0.1584-0.0898-0.36310.11470.00791.3162-0.0974-0.10180.74930.09461.509749.9768-7.470146.0297
100.0890.06890.26460.23370.40730.974-0.2277-0.9824-0.15721.3303-0.3231-0.093-0.1207-0.22570.01161.8033-0.01880.0181.1848-0.07741.02566.9659-28.2288-1.0976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 70:133)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 134:362)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 363:498)
4X-RAY DIFFRACTION4CHAIN B AND (RESID 71:222)
5X-RAY DIFFRACTION5CHAIN B AND (RESID 223:481)
6X-RAY DIFFRACTION6CHAIN B AND (RESID 482:502)
7X-RAY DIFFRACTION7CHAIN C AND (RESID 85:96)
8X-RAY DIFFRACTION8CHAIN D AND (RESID 85:96)
9X-RAY DIFFRACTION9CHAIN E AND (RESID 85:96)
10X-RAY DIFFRACTION10CHAIN F AND (RESID 85:96)

+
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