[English] 日本語
Yorodumi
- PDB-1h15: X-ray crystal structure of HLA-DRA1*0101/DRB5*0101 complexed with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h15
TitleX-ray crystal structure of HLA-DRA1*0101/DRB5*0101 complexed with a peptide from Epstein Barr Virus DNA polymerase
Components
  • (HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ...) x 2
  • DNA POLYMERASE
KeywordsIMMUNE SYSTEM/TRANSFERASE / COMPLEX (MHC-ANTIGEN) / IMMUNE SYSTEM / MHC / HLA / CLASS II / DR2 / DRB5 / EBV / DNA POLYMERASE / DNA-DIRECTED DNA POLYMERASE / IMMUNE SYSTEM-TRANSFERASE complex
Function / homology
Function and homology information


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 / nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II ...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 / nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / DNA replication proofreading / positive regulation of memory T cell differentiation / bidirectional double-stranded viral DNA replication / exonuclease activity / 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 / base-excision repair, gap-filling / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / 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 / positive regulation of T cell activation / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / cognition / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / early endosome membrane / adaptive immune response / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lysosome / immune response / Golgi membrane / lysosomal membrane / nucleotide binding / host cell nucleus / cell surface / DNA binding / extracellular exosome / plasma membrane
Similarity search - Function
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / 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 / : ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / 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 / : / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / 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 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Immunoglobulins / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen, DR alpha chain / DNA polymerase catalytic subunit / HLA class II histocompatibility antigen, DR beta 5 chain / HLA class II histocompatibility antigen, DR beta 5 chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
HUMAN HERPESVIRUS 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLang, H. / Jacobsen, H. / Ikemizu, S. / Andersson, C. / Harlos, K. / Madsen, L. / Hjorth, P. / Sondergaard, L. / Svejgaard, A. / Wucherpfennig, K. ...Lang, H. / Jacobsen, H. / Ikemizu, S. / Andersson, C. / Harlos, K. / Madsen, L. / Hjorth, P. / Sondergaard, L. / Svejgaard, A. / Wucherpfennig, K. / Stuart, D.I. / Bell, J.I. / Jones, E.Y. / Fugger, L.
CitationJournal: Nat.Immunol. / Year: 2002
Title: A Functional and Structural Basis for Tcr Cross-Reactivity in Multiple Sclerosis
Authors: Lang, H. / Jacobsen, H. / Ikemizu, S. / Andersson, C. / Harlos, K. / Madsen, L. / Hjorth, P. / Sondergaard, L. / Svejgaard, A. / Wucherpfennig, K. / Stuart, D.I. / Bell, J.I. / Jones, E.Y. / Fugger, L.
History
DepositionJul 2, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Jun 27, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
B: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR BETA 1 CHAIN
C: DNA POLYMERASE
D: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
E: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR BETA 1 CHAIN
F: DNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,12110
Polymers90,0336
Non-polymers1,0884
Water54030
1
A: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
B: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR BETA 1 CHAIN
C: DNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6625
Polymers45,0163
Non-polymers6462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-21 kcal/mol
Surface area18360 Å2
MethodPISA
2
D: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
E: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR BETA 1 CHAIN
F: DNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4595
Polymers45,0163
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-30.2 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.244, 179.244, 92.884
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

-
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ... , 2 types, 4 molecules ADBE

#1: Protein HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN / HLA-DRA / MAJOR HISTOCOMPATIBILITY COMPLEX A CHAIN


Mass: 21155.904 Da / Num. of mol.: 2 / Fragment: ALPHA CHAIN, RESIDUES 26-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P01903
#2: Protein HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR BETA 1 CHAIN / HLA-DRB1 / MAJOR HISTOCOMPATIBILITY COMPLEX B CHAIN


Mass: 22231.574 Da / Num. of mol.: 2 / Fragment: BETA CHAIN, RESIDUES 30-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q30126, UniProt: Q30154*PLUS

-
Protein/peptide / Non-polymers , 2 types, 32 molecules CF

#3: Protein/peptide DNA POLYMERASE / EPSTEIN BARR VIUS (EBV) DNA POLYMERASE


Mass: 1628.850 Da / Num. of mol.: 2 / Fragment: RESIDUES 628-641 / Source method: obtained synthetically
Details: THE PROTEIN OCCURS NATURALLY IN EBV BUT THE PEPTIDE WAS SYNTHESISED CHEMICALLY
Source: (synth.) HUMAN HERPESVIRUS 4 (Epstein-Barr virus) / References: UniProt: P03198, DNA-directed DNA polymerase
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

-
Sugars , 2 types, 4 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-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.: 3
Source method: isolated from a genetically manipulated source
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 protein modificationY
Sequence detailsRESIDUES 26-207 OF DATABASE SEQUENCE RESIDUES 30-219 OF DATABASE SEQUENCE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 52 %
Crystal growpH: 3.5
Details: 14% PEG 3550, 100MM GLYCINE AND 10MM TRIS AT PH 3.5-4.0.
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMTris1droppH7.4
210 mg/mlprotein1drop
314 %PEG33501reservoir
4100 mMglycine1reservoir
510 mMTris1reservoirpH3.5-4.0

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9686
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2001 / Details: MIRRORS
RadiationMonochromator: SI111 / SI311 CRYSTALS, LN2 COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 28750 / % possible obs: 94.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.414 / Net I/σ(I): 5.7
Reflection shellResolution: 3.1→3.3 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 1.1 / % possible all: 78.9
Reflection
*PLUS
Num. measured all: 166287
Reflection shell
*PLUS
% possible obs: 78.9 %

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SINGLE COPY OF 1FV1 (A AND B CHAINS) MINUS PEPTIDE

1fv1


Resolution: 3.1→19.88 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 64350.38 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1415 4.9 %RANDOM
Rwork0.256 ---
obs0.256 28750 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 60.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å212.75 Å20 Å2
2--2.37 Å20 Å2
3----4.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a1.07 Å0.87 Å
Refinement stepCycle: LAST / Resolution: 3.1→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6320 0 70 30 6420
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.522.5
X-RAY DIFFRACTIONc_mcangle_it4.353.5
X-RAY DIFFRACTIONc_scbond_it3.543
X-RAY DIFFRACTIONc_scangle_it5.94.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.479 197 5.4 %
Rwork0.456 3455 -
obs--71.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 3.1 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.31
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
LS refinement shell
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 3.3 Å

+
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