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- PDB-3pgd: Crystal Structure of HLA-DR1 with CLIP106-120, canonical peptide ... -

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Basic information

Entry
Database: PDB / ID: 3pgd
TitleCrystal Structure of HLA-DR1 with CLIP106-120, canonical peptide orientation
Components
  • HLA class II histocompatibility antigen gamma chain
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DRB1-1 beta chain
KeywordsIMMUNE SYSTEM / MHC class II / MHC II / self antigen / invariant chain / CLIP
Function / homology
Function and homology information


negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation / macrophage migration inhibitory factor binding / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization ...negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation / macrophage migration inhibitory factor binding / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization / macrophage migration inhibitory factor receptor complex / positive regulation of cytokine-mediated signaling pathway / regulation of interleukin-4 production / regulation of interleukin-10 production / T cell activation involved in immune response / 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 / positive regulation of type 2 immune response / T cell selection / regulation of T-helper cell differentiation / negative thymic T cell selection / positive regulation of prostaglandin biosynthetic process / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / negative regulation of viral entry into host cell / MHC class II receptor activity / MHC class II protein binding / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / negative regulation of mature B cell apoptotic process / positive regulation of memory T cell differentiation / positive thymic T cell selection / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / inflammatory response to antigenic stimulus / vacuole / positive regulation of neutrophil chemotaxis / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of macrophage cytokine production / prostaglandin biosynthetic process / positive regulation of T cell differentiation / intermediate filament / cytokine receptor activity / regulation of macrophage activation / transport vesicle membrane / polysaccharide binding / T-helper 1 type immune response / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cytokine binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / response to type II interferon / nitric-oxide synthase binding / positive regulation of insulin secretion involved in cellular response to glucose stimulus / chaperone cofactor-dependent protein refolding / negative regulation of DNA damage response, signal transduction by p53 class mediator / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / antigen processing and presentation / immunoglobulin mediated immune response / PD-1 signaling / epidermis development / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / protein folding chaperone / positive regulation of B cell proliferation / positive regulation of chemokine production / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / multivesicular body / lysosomal lumen / negative regulation of cell migration / trans-Golgi network membrane / positive regulation of interleukin-8 production / lumenal side of endoplasmic reticulum membrane / Cell surface interactions at the vascular wall / protein tetramerization / intracellular protein transport / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / peptide antigen assembly with MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / peptide antigen binding / positive regulation of interleukin-6 production / 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 peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / positive regulation of T cell activation
Similarity search - Function
MHC class II-associated invariant chain, trimerisation / MHC class II-associated invariant chain/CLIP, MHC II-interacting / MHC class II-associated invariant chain / MHC class II-associated invariant chain, trimerisation domain superfamily / HLA class II histocompatibility antigen, gamma subunit / Class II MHC-associated invariant chain trimerisation domain / CLIP, MHC2 interacting / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily ...MHC class II-associated invariant chain, trimerisation / MHC class II-associated invariant chain/CLIP, MHC II-interacting / MHC class II-associated invariant chain / MHC class II-associated invariant chain, trimerisation domain superfamily / HLA class II histocompatibility antigen, gamma subunit / Class II MHC-associated invariant chain trimerisation domain / CLIP, MHC2 interacting / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / 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 / HLA class II histocompatibility antigen gamma chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.72 Å
AuthorsGunther, S. / Schlundt, A. / Sticht, J. / Roske, Y. / Heinemann, U. / Wiesmuller, K.-H. / Jung, G. / Falk, K. / Rotzschke, O. / Freund, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Bidirectional binding of invariant chain peptides to an MHC class II molecule.
Authors: Gunther, S. / Schlundt, A. / Sticht, J. / Roske, Y. / Heinemann, U. / Wiesmuller, K.H. / Jung, G. / Falk, K. / Rotzschke, O. / Freund, C.
History
DepositionNov 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
C: HLA class II histocompatibility antigen gamma chain
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1-1 beta chain
F: HLA class II histocompatibility antigen gamma chain


Theoretical massNumber of molelcules
Total (without water)94,3516
Polymers94,3516
Non-polymers00
Water3,117173
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
C: HLA class II histocompatibility antigen gamma chain


Theoretical massNumber of molelcules
Total (without water)47,1753
Polymers47,1753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1-1 beta chain
F: HLA class II histocompatibility antigen gamma chain


Theoretical massNumber of molelcules
Total (without water)47,1753
Polymers47,1753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.449, 94.449, 275.535
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21E
12A
22D
13C
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain B and (resseq 0:106 or resseq 113:190 ) and (not element H) and (not element D)B0 - 106
121chain B and (resseq 0:106 or resseq 113:190 ) and (not element H) and (not element D)B113 - 190
211chain E and (resseq 0:106 or resseq 113:190 ) and (not element H) and (not element D)E0 - 106
221chain E and (resseq 0:106 or resseq 113:190 ) and (not element H) and (not element D)E113 - 190
112chain A and (resseq 4:44 or resseq 52:181 ) and (not element H) and (not element D)A4 - 44
122chain A and (resseq 4:44 or resseq 52:181 ) and (not element H) and (not element D)A52 - 181
212chain D and (resseq 4:44 or resseq 52:181 ) and (not element H) and (not element D)D4 - 44
222chain D and (resseq 4:44 or resseq 52:181 ) and (not element H) and (not element D)D52 - 181
113chain C and (resseq 106:120 ) and (not element H) and (not element D)C0
213chain F and (resseq 106:120 ) and (not element H) and (not element D)F0

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.999877, 0.012198, -0.009866), (0.011905, -0.999503, -0.029205), (-0.010217, 0.029084, -0.999525)2.27236, -93.242401, 70.976097
2given(0.999856, 0.009774, -0.013877), (0.009425, -0.999642, -0.025046), (-0.014117, 0.024911, -0.99959)2.3906, -93.574402, 70.697998
3given(0.999552, 0.020355, -0.021926), (0.019915, -0.999599, -0.020116), (-0.022327, 0.019671, -0.999557)3.38751, -93.802498, 70.395302

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Components

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


Mass: 22353.223 Da / Num. of mol.: 2 / Fragment: UNP residues 26-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-1 beta chain / MHC class II antigen DRB1*1 / DR-1 / DR1


Mass: 23087.791 Da / Num. of mol.: 2 / Fragment: UNP residues 30-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04229, UniProt: P01911*PLUS
#3: Protein/peptide HLA class II histocompatibility antigen gamma chain / HLA-DR antigens-associated invariant chain / Ia antigen-associated invariant chain / Ii / p33


Mass: 1734.263 Da / Num. of mol.: 2 / Fragment: UNP residues 106-120 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04233
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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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: 3.26 Å3/Da / Density % sol: 62.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 3350, NaCitrate, BisTris propane, pH 6.5, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: Rayonix / Detector: CCD / Date: Jun 9, 2010
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.72→35 Å / Num. all: 34529 / Num. obs: 34493 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 45.618 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 12.19
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.72-2.790.8732.2171012513100
2.79-2.870.7082.8167932421100
2.87-2.950.583.3168412383100
2.95-3.040.5043.9166852308100
3.04-3.140.4075163482224100
3.14-3.250.2926.9162602189100
3.25-3.370.2288.6157422095100
3.37-3.510.17210.9154402024100
3.51-3.670.14412.9148361923100
3.67-3.850.12914.3145491867100
3.85-4.050.10716.9141641789100
4.05-4.30.08819.513610170099.9
4.3-4.60.07423.3128101581100
4.6-4.970.06924.9124121510100
4.97-5.440.07122.6113731366100
5.44-6.080.07221107101277100
6.08-7.020.06820.49461112099.9
7.02-8.60.053247993979100
8.6-12.160.041285988777100
12.16-350.03822.1291644793.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 57.7 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.72 Å33.52 Å
Translation2.72 Å33.52 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→33.393 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2416 1725 5.01 %RANDOM
Rwork0.196 ---
obs0.1983 34451 99.86 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.656 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso max: 121.92 Å2 / Biso mean: 44.5183 Å2 / Biso min: 10.48 Å2
Baniso -1Baniso -2Baniso -3
1-3.4245 Å20 Å2-0 Å2
2--3.4245 Å2-0 Å2
3----6.8491 Å2
Refinement stepCycle: LAST / Resolution: 2.72→33.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6151 0 0 173 6324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096321
X-RAY DIFFRACTIONf_angle_d1.1328588
X-RAY DIFFRACTIONf_chiral_restr0.07931
X-RAY DIFFRACTIONf_plane_restr0.0051118
X-RAY DIFFRACTIONf_dihedral_angle_d17.1412304
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1503X-RAY DIFFRACTIONPOSITIONAL0.153
12E1503X-RAY DIFFRACTIONPOSITIONAL0.153
21A1387X-RAY DIFFRACTIONPOSITIONAL0.131
22D1387X-RAY DIFFRACTIONPOSITIONAL0.131
31C116X-RAY DIFFRACTIONPOSITIONAL0.069
32F116X-RAY DIFFRACTIONPOSITIONAL0.069
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 (%)
2.72-2.81720.37331680.278431913359100
2.8172-2.930.30041690.265432163385100
2.93-3.06320.2971700.235332323402100
3.0632-3.22460.31261690.225732053374100
3.2246-3.42650.26041700.210232283398100
3.4265-3.69070.24271710.196632543425100
3.6907-4.06150.21661720.178632603432100
4.0615-4.64790.20221730.146932813454100
4.6479-5.85080.21121770.164433583535100
5.8508-33.3930.20861860.20313501368799

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