[English] 日本語
Yorodumi
- PDB-1muj: Crystal structure of murine class II MHC I-Ab in complex with a h... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1muj
TitleCrystal structure of murine class II MHC I-Ab in complex with a human CLIP peptide
Components
  • CLIP peptide
  • H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A BETA CHAIN
  • H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-B ALPHA CHAIN
KeywordsIMMUNE SYSTEM / I-AB / CLIP / COMPLEX / ANTIGEN
Function / homology
Function and homology information


positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / 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 antigen processing and presentation / positive regulation of alpha-beta T cell activation / 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 / positive regulation of T-helper 1 type immune response / T cell activation involved in immune response / protein antigen binding / positive regulation of type 2 immune response / T cell selection / negative thymic T cell selection / positive regulation of prostaglandin biosynthetic process / negative regulation of viral entry into host cell / antigen processing and presentation of peptide antigen / B cell affinity maturation / MHC class II protein binding / negative regulation of mature B cell apoptotic process / positive thymic T cell selection / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of neutrophil chemotaxis / positive regulation of macrophage cytokine production / vacuole / prostaglandin biosynthetic process / positive regulation of T cell differentiation / cytokine receptor activity / regulation of macrophage activation / transport vesicle membrane / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / nitric-oxide synthase binding / cytokine binding / response to type II interferon / antigen processing and presentation / negative regulation of DNA damage response, signal transduction by p53 class mediator / chaperone cofactor-dependent protein refolding / toxic substance binding / immunoglobulin mediated immune response / negative regulation of T cell proliferation / positive regulation of chemokine production / positive regulation of B cell proliferation / protein folding chaperone / MHC class II antigen presentation / multivesicular body / negative regulation of cell migration / lysosomal lumen / trans-Golgi network membrane / positive regulation of interleukin-8 production / lumenal side of endoplasmic reticulum membrane / Cell surface interactions at the vascular wall / intracellular protein transport / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / cellular response to type II interferon / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / positive regulation of interleukin-6 production / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of immune response / positive regulation of fibroblast proliferation / late endosome / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / amyloid-beta binding / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / early endosome / protein stabilization / positive regulation of protein phosphorylation / immune response / lysosomal membrane / external side of plasma membrane / Golgi membrane / ubiquitin protein ligase binding / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / Golgi apparatus / cell surface / protein-containing complex
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 gamma chain / H-2 class II histocompatibility antigen, A-B alpha chain / H-2 class II histocompatibility antigen, A beta chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsZhu, Y. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of MHC class II I-Ab in complex with a human CLIP peptide: Prediction of an I-Ab peptide-binding motif
Authors: Zhu, Y. / Rudensky, A.Y. / Teyton, A.L. / Wilson, I.A.
History
DepositionSep 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-B ALPHA CHAIN
B: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A BETA CHAIN
C: CLIP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7615
Polymers48,3183
Non-polymers4422
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-39 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.647, 88.065, 83.740
Angle α, β, γ (deg.)90.00, 92.48, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-B ALPHA CHAIN


Mass: 21428.828 Da / Num. of mol.: 1
Fragment: EXTRACELLULAR ALPHA-1 and EXTRACELLULAR ALPHA-2 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P14434
#2: Protein H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A BETA CHAIN


Mass: 23192.846 Da / Num. of mol.: 1
Fragment: EXTRACELLULAR BETA-1 and EXTRACELLULAR BETA-2 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P14483
#3: Protein/peptide CLIP peptide


Mass: 3696.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The peptide was covalently linked to the N-terminus of chain B.
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P04233*PLUS
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG3000, Sodium Chloride, Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTris1reservoirpH7.5
2200 mM1reservoirNaCl
322.5 %PEG30001reservoir
45 %(v/v)MPD1reservoir
55-10 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 17, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.15→33.06 Å / Num. obs: 24657 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.87 % / Biso Wilson estimate: 32.6 Å2 / Limit h max: 31 / Limit h min: -31 / Limit k max: 43 / Limit k min: -31 / Limit l max: 41 / Limit l min: 0 / Observed criterion F max: 1792626.54 / Observed criterion F min: 0.63 / Rsym value: 0.038 / Net I/σ(I): 24.1
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.15723 / Mean I/σ(I) obs: 1.65 / Num. unique all: 2403 / Rsym value: 0.544 / % possible all: 97
Reflection
*PLUS
Highest resolution: 2.15 Å / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 97 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.7

-
Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→33.06 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1090 4.8 %RANDOM
Rwork0.22 ---
all0.22 25144 --
obs0.22 22763 90.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 60.968 Å2 / ksol: 0.330054 e/Å3
Displacement parametersBiso max: 129.3 Å2 / Biso mean: 62.36 Å2 / Biso min: 28.74 Å2
Baniso -1Baniso -2Baniso -3
1--12.48 Å20 Å21.35 Å2
2--10.06 Å20 Å2
3---2.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.49 Å
Luzzati d res high-2.15
Refinement stepCycle: LAST / Resolution: 2.15→33.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3112 0 28 171 3311
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg26.4
X-RAY DIFFRACTIONx_torsion_impr_deg0.79
X-RAY DIFFRACTIONx_dihedral_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d26.4
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.15-2.250.3971173.80.39722840.0373113240177.1
2.25-2.370.3541173.70.35623950.0333137251280.1
2.37-2.510.321284.10.32325850.0283125271386.8
2.51-2.710.3061494.70.30927050.0253160285490.3
2.71-2.980.2641424.50.26428340.0223127297695.2
2.98-3.410.2411404.40.23829310.023153307197.4
3.41-4.30.1921344.30.18829540.0173145308898.2
4.3-33.060.1731635.10.17329850.0143209314898.1
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.param
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shell
*PLUS
Lowest resolution: 2.23 Å / Rfactor Rfree: 0.37 / Rfactor Rwork: 0.36

+
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://pdbjlvh1.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