[English] 日本語
Yorodumi
- PDB-7o00: Crystal structure of HLA-DR4 in complex with a HSP70 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7o00
TitleCrystal structure of HLA-DR4 in complex with a HSP70 peptide
Components
  • (HLA class II histocompatibility ...) x 2
  • Chaperone protein DnaK
KeywordsIMMUNE SYSTEM / Complex / MHCII
Function / homology
Function and homology information


bacterial extracellular vesicle / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation ...bacterial extracellular vesicle / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / T cell receptor binding / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / ATP-dependent protein folding chaperone / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / cognition / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / unfolded protein binding / Downstream TCR signaling / early endosome membrane / adaptive immune response / lysosome / endosome membrane / immune response / Golgi membrane / lysosomal membrane / cell surface / extracellular exosome / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Chaperone DnaK / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. ...Chaperone DnaK / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / MHC classes I/II-like antigen recognition protein / : / ATPase, nucleotide binding domain / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
HLA class II histocompatibility antigen DR beta chain / Chaperone protein DnaK / HLA class II histocompatibility antigen, DR alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Mycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsGe, C. / Holmdahl, R.
Funding support Sweden, 3items
OrganizationGrant numberCountry
The Swedish Foundation for Strategic Research Sweden
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Ann Rheum Dis / Year: 2022
Title: Key interactions in the trimolecular complex consisting of the rheumatoid arthritis-associated DRB1*04:01 molecule, the major glycosylated collagen II peptide and the T-cell receptor.
Authors: Ge, C. / Weisse, S. / Xu, B. / Dobritzsch, D. / Viljanen, J. / Kihlberg, J. / Do, N.N. / Schneider, N. / Lanig, H. / Holmdahl, R. / Burkhardt, H.
History
DepositionMar 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: HLA class II histocompatibility antigen, DR alpha chain
BBB: HLA class II histocompatibility antigen DR beta chain
CCC: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9835
Polymers44,3383
Non-polymers6462
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-31 kcal/mol
Surface area18230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.230, 76.230, 170.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

-
Components

-
HLA class II histocompatibility ... , 2 types, 2 molecules AAABBB

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 20598.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Homo sapiens (human) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen DR beta chain / MHC class II antigen


Mass: 22218.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Homo sapiens (human) / References: UniProt: A0A1V1IGJ9

-
Protein/peptide / Non-polymers , 2 types, 81 molecules CCC

#3: Protein/peptide Chaperone protein DnaK / HSP70 / Heat shock 70 kDa protein / Heat shock protein 70


Mass: 1520.729 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria) / References: UniProt: A1KFH2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

-
Sugars , 2 types, 2 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 290 K / Method: evaporation
Details: 0.03 M of each divalent cation (12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD), 0.1 M MOPS/HEPES-Na pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.24→56.89 Å / Num. obs: 25047 / % possible obs: 99.8 % / Redundancy: 25.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.066 / Rrim(I) all: 0.246 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.96-56.8920.20.0634870.9990.0180.065
2.24-2.3126.63.47422410.6350.9613.605

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J8H

1j8h


Resolution: 2.24→51.453 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.217 / WRfactor Rwork: 0.175 / SU B: 16.37 / SU ML: 0.179 / Average fsc free: 0.88 / Average fsc work: 0.8927 / Cross valid method: FREE R-VALUE / ESU R: 0.284 / ESU R Free: 0.221
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2422 1105 4.919 %
Rwork0.1985 21358 -
all0.201 --
obs-22463 89.691 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 53.581 Å2
Baniso -1Baniso -2Baniso -3
1--0.036 Å20 Å20 Å2
2---0.036 Å20 Å2
3---0.071 Å2
Refinement stepCycle: LAST / Resolution: 2.24→51.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3057 0 42 80 3179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133190
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172888
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.6744342
X-RAY DIFFRACTIONr_angle_other_deg1.2131.5946649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2635366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.62921.917193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.35215501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5791524
X-RAY DIFFRACTIONr_chiral_restr0.070.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023577
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02784
X-RAY DIFFRACTIONr_nbd_refined0.1990.2508
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.22723
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21451
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21714
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2103
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2010.211
X-RAY DIFFRACTIONr_nbd_other0.190.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2280.27
X-RAY DIFFRACTIONr_mcbond_it1.7643.4971479
X-RAY DIFFRACTIONr_mcbond_other1.7643.4961478
X-RAY DIFFRACTIONr_mcangle_it2.8095.2371840
X-RAY DIFFRACTIONr_mcangle_other2.8085.2381841
X-RAY DIFFRACTIONr_scbond_it2.4863.8911710
X-RAY DIFFRACTIONr_scbond_other2.4843.8911710
X-RAY DIFFRACTIONr_scangle_it4.0085.7152502
X-RAY DIFFRACTIONr_scangle_other4.0075.7152503
X-RAY DIFFRACTIONr_lrange_it5.84439.8473288
X-RAY DIFFRACTIONr_lrange_other5.82639.6843275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.2980.396550.3711257X-RAY DIFFRACTION72.9294
2.298-2.3610.353760.3481262X-RAY DIFFRACTION76.0227
2.361-2.4290.339790.3151269X-RAY DIFFRACTION77.8741
2.429-2.5040.327740.31270X-RAY DIFFRACTION80.7207
2.504-2.5860.313800.2751252X-RAY DIFFRACTION82.7843
2.586-2.6770.308600.261305X-RAY DIFFRACTION87.2205
2.677-2.7780.289670.2241293X-RAY DIFFRACTION88.8889
2.778-2.8910.238780.2141271X-RAY DIFFRACTION91.7063
2.891-3.0190.239570.2041285X-RAY DIFFRACTION95.1098
3.019-3.1660.299590.1981257X-RAY DIFFRACTION96.3397
3.166-3.3370.196440.1771202X-RAY DIFFRACTION97.2678
3.337-3.5390.212590.1731146X-RAY DIFFRACTION98.3673
3.539-3.7830.226670.1691073X-RAY DIFFRACTION99.4764
3.783-4.0860.201490.1641040X-RAY DIFFRACTION99.543
4.086-4.4740.15400.15970X-RAY DIFFRACTION99.7038
4.474-50.193440.152871X-RAY DIFFRACTION99.8908
5-5.770.213400.178778X-RAY DIFFRACTION99.8779
5.77-7.0560.232270.199683X-RAY DIFFRACTION99.5792
7.056-9.9360.262300.188539X-RAY DIFFRACTION100
9.936-51.4530.381200.293335X-RAY DIFFRACTION98.0663
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)
11.53180.27421.11641.3338-0.01153.5374-0.1399-0.1090.2014-0.06070.09570.065-0.299-0.09130.04420.06660.0167-0.00040.12080.00580.0416-20.477542.6716-5.7098
21.68450.28820.55131.51220.69373.7468-0.04430.0141-0.1404-0.06440.0955-0.08970.20630.4918-0.05110.02570.03830.01370.19840.02630.0333-8.33430.5854-4.2136
35.05116.33663.699710.09665.40734.07970.1799-0.0574-0.05840.5862-0.0442-0.03440.23150.0495-0.13570.12820.04970.04380.21780.02910.1933-18.917934.323715.6546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA4 - 180
2X-RAY DIFFRACTION1ALLAaA181
3X-RAY DIFFRACTION2ALLBBB2 - 190
4X-RAY DIFFRACTION3ALLCCC1 - 14

+
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