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- PDB-3c5j: Crystal structure of HLA DR52c -

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Basic information

Entry
Database: PDB / ID: 3c5j
TitleCrystal structure of HLA DR52c
Components
  • Elongation factor 1-alpha 2
  • HLA class II histocompatibility antigen, DR alpha chain
  • MHC class II antigen
KeywordsMEMBRANE PROTEIN / HLA / MHC class II / Glycoprotein / Immune response / Membrane / MHC II / Transmembrane / Elongation factor / GTP-binding / Methylation / Nucleotide-binding / Nucleus / Phosphoprotein / Protein biosynthesis
Function / homology
Function and homology information


cytoplasmic side of lysosomal membrane / Eukaryotic Translation Elongation / : / eukaryotic translation elongation factor 1 complex / regulation of chaperone-mediated autophagy / 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 / translation factor activity, RNA binding ...cytoplasmic side of lysosomal membrane / Eukaryotic Translation Elongation / : / eukaryotic translation elongation factor 1 complex / regulation of chaperone-mediated autophagy / 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 / translation factor activity, RNA binding / 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 / translational elongation / polysaccharide binding / positive regulation of lipid kinase activity / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / plasma membrane => GO:0005886 / Generation of second messenger molecules / immunological synapse / PD-1 signaling / translation elongation factor activity / type II interferon-mediated signaling pathway / MHC class II antigen presentation / T cell receptor binding / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / 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 / adaptive immune response / lysosome / endosome membrane / immune response / translation / positive regulation of apoptotic process / lysosomal membrane / Golgi membrane / GTPase activity / synapse / GTP binding / protein kinase binding / cell surface / signal transduction / extracellular exosome / membrane / plasma membrane / cytoplasm
Similarity search - Function
Translation elongation factor EF1A, eukaryotic/archaeal / 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 ...Translation elongation factor EF1A, eukaryotic/archaeal / 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 / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / 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 / Translation protein, beta-barrel domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class II antigen / HLA class II histocompatibility antigen, DR alpha chain / Elongation factor 1-alpha 2 / HLA class II histocompatibility antigen, DR beta 3 chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsDai, S. / Kappler, J.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: The structure of HLA-DR52c: comparison to other HLA-DRB3 alleles.
Authors: Dai, S. / Crawford, F. / Marrack, P. / Kappler, J.W.
History
DepositionJan 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
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_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: MHC class II antigen
C: Elongation factor 1-alpha 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1366
Polymers44,5973
Non-polymers5383
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
MethodPISA
2
A: HLA class II histocompatibility antigen, DR alpha chain
B: MHC class II antigen
C: Elongation factor 1-alpha 2
hetero molecules

A: HLA class II histocompatibility antigen, DR alpha chain
B: MHC class II antigen
C: Elongation factor 1-alpha 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,27112
Polymers89,1946
Non-polymers1,0776
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+3/41
Buried area17090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.380, 83.380, 132.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 21084.826 Da / Num. of mol.: 1 / Fragment: UNP residues 25-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P01903
#2: Protein MHC class II antigen


Mass: 22121.693 Da / Num. of mol.: 1 / Fragment: UNP residues 30-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB3 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q6YJU6, UniProt: B8YAC7*PLUS

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Protein/peptide / Sugars , 2 types, 3 molecules C

#3: Protein/peptide Elongation factor 1-alpha 2 / EF-1-alpha-2 / Elongation factor 1 A-2 / eEF1A-2 / Statin S1


Mass: 1390.607 Da / Num. of mol.: 1 / Fragment: UNP residues 343-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EEF1A2, EEF1AL, STN / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q05639
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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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Non-polymers , 2 types, 455 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCHAIN C AND CHAIN B ARE FUSED TOGETHER THROUGH A LINKER ( GGGGSLVPRGSGGGGS ). HOWEVER THIS LINKER ...CHAIN C AND CHAIN B ARE FUSED TOGETHER THROUGH A LINKER ( GGGGSLVPRGSGGGGS ). HOWEVER THIS LINKER IS DISORDERED

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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: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6 M ammonium sulfate, pH 7.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2002 / Details: Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 42787 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.064 / Χ2: 1.457 / Net I/σ(I): 14.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.803 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3832 / Χ2: 1.553 / % possible all: 87.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementResolution: 1.8→41.69 Å / Rfactor Rfree error: 0.005 / FOM work R set: 0.84 / Data cutoff high absF: 2282868.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2141 5 %RANDOM
Rwork0.202 ---
obs-42672 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.166 Å2 / ksol: 0.398 e/Å3
Displacement parametersBiso mean: 29.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å20 Å2
2--1.37 Å20 Å2
3----2.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→41.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3066 0 33 454 3553
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 351 5.5 %
Rwork0.279 6084 -
all-6435 -
obs-6084 89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2water_rep.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3ion.param&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4carbohydrate.param&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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