[English] 日本語
Yorodumi
- PDB-3rwi: Rhesus macaque MHC class I molecule Mamu-B*17-GW10 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rwi
TitleRhesus macaque MHC class I molecule Mamu-B*17-GW10
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Major histocompatibility complex class IMHC class I
  • Vif GW10 peptide from Virion infectivity factor
KeywordsIMMUNE SYSTEM / antigenic peptides / T lymphocytes / immune response
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / viral life cycle / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / ER to Golgi transport vesicle membrane / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity ...antigen processing and presentation of peptide antigen via MHC class I / viral life cycle / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / ER to Golgi transport vesicle membrane / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / early endosome membrane / host cell cytoplasm / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / host cell plasma membrane / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Retroviral Vif (Viral infectivity) protein / Retroviral Vif (Viral infectivity) protein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like ...Retroviral Vif (Viral infectivity) protein / Retroviral Vif (Viral infectivity) protein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / Virion infectivity factor / Major histocompatibility complex class I
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Simian immunodeficiency virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.009 Å
AuthorsWu, Y. / Gao, F. / Liu, J. / Qi, J.X. / Price, D.A. / Gao, G.F.
CitationJournal: J.Immunol. / Year: 2011
Title: Structural basis of diverse peptide accommodation by the rhesus macaque MHC class I molecule Mamu-B*17: insights into immune protection from simian immunodeficiency virus
Authors: Wu, Y. / Gao, F. / Liu, J. / Qi, J.X. / Gostick, E. / Price, D.A. / Gao, G.F.
History
DepositionMay 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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: Major histocompatibility complex class I
B: Beta-2-microglobulin
C: Vif GW10 peptide from Virion infectivity factor


Theoretical massNumber of molelcules
Total (without water)44,8613
Polymers44,8613
Non-polymers00
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-17 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.456, 45.051, 82.057
Angle α, β, γ (deg.)90.00, 95.99, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11B-130-

HOH

-
Components

#1: Protein Major histocompatibility complex class I / MHC class I


Mass: 32025.082 Da / Num. of mol.: 1 / Fragment: residues 24-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: MHCI-B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GJ77
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11660.079 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: Q6V7J5
#3: Protein/peptide Vif GW10 peptide from Virion infectivity factor


Mass: 1176.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthtic peptide / Source: (synth.) Simian immunodeficiency virus / References: UniProt: Q89490
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.15 %

-
Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.009→50 Å / Num. obs: 32167 / Biso Wilson estimate: 26.21 Å2

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.4_486) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BVO

2bvo


Resolution: 2.009→24.399 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8667 / SU ML: 0.25 / σ(F): 1.36 / Phase error: 20.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2099 1642 5.11 %
Rwork0.1735 --
obs0.1755 32113 95.6 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.168 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso max: 132.33 Å2 / Biso mean: 31.6043 Å2 / Biso min: 5.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.6023 Å2-0 Å20.0633 Å2
2---0.7726 Å20 Å2
3---0.1703 Å2
Refinement stepCycle: LAST / Resolution: 2.009→24.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3167 0 0 445 3612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013393
X-RAY DIFFRACTIONf_angle_d0.8494432
X-RAY DIFFRACTIONf_chiral_restr0.062434
X-RAY DIFFRACTIONf_plane_restr0.003592
X-RAY DIFFRACTIONf_dihedral_angle_d12.9261212
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0088-2.08060.27571410.2082939308093
2.0806-2.16380.24511560.19142985314194
2.1638-2.26220.27061590.19342973313294
2.2622-2.38140.25261890.19162962315195
2.3814-2.53050.22361560.17893045320195
2.5305-2.72560.20671640.17673033319796
2.7256-2.99940.24641870.1883071325897
2.9994-3.43240.23611460.18853119326597
3.4324-4.32060.1791530.15513169332298
4.3206-24.40070.1571910.15043175336697
Refinement TLS params.Method: refined / Origin x: -4.5109 Å / Origin y: -0.1184 Å / Origin z: -20.6266 Å
111213212223313233
T0.0621 Å2-0.0324 Å2-0.0035 Å2-0.0692 Å20.0309 Å2--0.0304 Å2
L1.0973 °20.019 °20.2515 °2-0.2416 °2-0.0805 °2--0.2059 °2
S-0.0538 Å °0.2502 Å °0.0975 Å °0.0031 Å °0.0172 Å °0.0197 Å °-0.0283 Å °0.0733 Å °0.0347 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 276
2X-RAY DIFFRACTION1ALLA277 - 566
3X-RAY DIFFRACTION1ALLC1 - 10
4X-RAY DIFFRACTION1ALLC18 - 436
5X-RAY DIFFRACTION1ALLB1 - 99
6X-RAY DIFFRACTION1ALLB100 - 445

+
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