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- PDB-5v4n: Structure of HLA-DR1 with bound alpha3(135-145) peptide -

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Basic information

Entry
Database: PDB / ID: 5v4n
TitleStructure of HLA-DR1 with bound alpha3(135-145) peptide
Components
  • HLA-DRA1
  • alpha3(135-145)-HLA-DRB1*01:01
KeywordsIMMUNE SYSTEM / HLA-DR / immune complex / antigen presenation
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / 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 ...regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / 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 / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / inflammatory response to antigenic stimulus / intermediate filament / transport vesicle membrane / T-helper 1 type immune response / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / negative regulation of inflammatory response to antigenic stimulus / negative regulation of T cell proliferation / MHC class II antigen presentation / detection of bacterium / T cell receptor binding / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / adaptive immune response / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / immune response / positive regulation of protein phosphorylation / lysosomal membrane / external side of plasma membrane / Golgi membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / 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 / MHC classes I/II-like antigen recognition protein ...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 / 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 / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen, DRB1 beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.405 Å
AuthorsPetersen, J. / Rossjohn, J.
CitationJournal: Nature / Year: 2017
Title: Dominant protection from HLA-linked autoimmunity by antigen-specific regulatory T cells.
Authors: Ooi, J.D. / Petersen, J. / Tan, Y.H. / Huynh, M. / Willett, Z.J. / Ramarathinam, S.H. / Eggenhuizen, P.J. / Loh, K.L. / Watson, K.A. / Gan, P.Y. / Alikhan, M.A. / Dudek, N.L. / Handel, A. / ...Authors: Ooi, J.D. / Petersen, J. / Tan, Y.H. / Huynh, M. / Willett, Z.J. / Ramarathinam, S.H. / Eggenhuizen, P.J. / Loh, K.L. / Watson, K.A. / Gan, P.Y. / Alikhan, M.A. / Dudek, N.L. / Handel, A. / Hudson, B.G. / Fugger, L. / Power, D.A. / Holt, S.G. / Coates, P.T. / Gregersen, J.W. / Purcell, A.W. / Holdsworth, S.R. / La Gruta, N.L. / Reid, H.H. / Rossjohn, J. / Kitching, A.R.
History
DepositionMar 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2May 24, 2017Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA-DRA1
C: alpha3(135-145)-HLA-DRB1*01:01
D: HLA-DRA1
F: alpha3(135-145)-HLA-DRB1*01:01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7227
Polymers93,0584
Non-polymers6643
Water0
1
A: HLA-DRA1
C: alpha3(135-145)-HLA-DRB1*01:01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7503
Polymers46,5292
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-28 kcal/mol
Surface area18060 Å2
MethodPISA
2
D: HLA-DRA1
F: alpha3(135-145)-HLA-DRB1*01:01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9714
Polymers46,5292
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-26 kcal/mol
Surface area18310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.086, 118.410, 120.875
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA-DRA1 / MHC class II antigen DRA


Mass: 21919.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01903
#2: Protein alpha3(135-145)-HLA-DRB1*01:01 / MHC class II antigen DRB1*1 / DR1 / MHC class II antigen DRB1*1 / DR1 / MHC class II antigen DRB1*1 ...MHC class II antigen DRB1*1 / DR1 / MHC class II antigen DRB1*1 / DR1 / MHC class II antigen DRB1*1 / DR1 / chimeric construct / MHC class II antigen DRB1*1 / DR1 / chimeric construct


Mass: 24609.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04229, UniProt: P01911*PLUS
#3: 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 / N-Acetylglucosamine


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

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 23% PEG 3350, 0.1M KNO3, and 0.1M bis-tris-propane (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.405→53.831 Å / Num. obs: 16628 / % possible obs: 99 % / Redundancy: 2 % / CC1/2: 0.942 / Rmerge(I) obs: 0.1099 / Net I/σ(I): 6.04
Reflection shellRedundancy: 2 % / Rmerge(I) obs: 0.3648 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1610 / CC1/2: 0.651 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QXA

3qxa


Resolution: 3.405→53.831 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.08
RfactorNum. reflection% reflection
Rfree0.2629 837 5.04 %
Rwork0.2121 --
obs0.2146 16595 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.405→53.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6152 0 42 0 6194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026381
X-RAY DIFFRACTIONf_angle_d0.6558699
X-RAY DIFFRACTIONf_dihedral_angle_d16.333728
X-RAY DIFFRACTIONf_chiral_restr0.046938
X-RAY DIFFRACTIONf_plane_restr0.0041128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4051-3.61840.31021510.26492541X-RAY DIFFRACTION99
3.6184-3.89770.3151120.25072619X-RAY DIFFRACTION100
3.8977-4.28970.28231450.20442585X-RAY DIFFRACTION99
4.2897-4.91010.21171500.16652610X-RAY DIFFRACTION100
4.9101-6.18480.23361540.1922637X-RAY DIFFRACTION100
6.1848-53.83770.26971250.2232766X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 13.411 Å / Origin y: 109.1652 Å / Origin z: 136.7139 Å
111213212223313233
T0.3318 Å2-0.068 Å20.0311 Å2-0.2931 Å2-0.0053 Å2--0.3746 Å2
L0.7765 °2-0.431 °20.2357 °2-1.2944 °2-0.5446 °2--1.8292 °2
S0.0551 Å °0.0141 Å °-0.0082 Å °-0.112 Å °-0.1382 Å °-0.2292 Å °0.1745 Å °0.0174 Å °0.0797 Å °
Refinement TLS groupSelection details: all

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