[English] 日本語
Yorodumi
- PDB-1k2d: Crystal structure of the autoimmune MHC class II I-Au complexed w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k2d
TitleCrystal structure of the autoimmune MHC class II I-Au complexed with myelin basic protein 1-11 at 2.2A
Components
  • H-2 class II histocompatibility antigen, A-U alpha chain
  • H-2 class II histocompatibility antigen, A-U beta chain
  • Myelin Basic Protein peptide with 8 residue linker peptide
KeywordsIMMUNE SYSTEM / MHC class II / I-Au / H-2u / autoimmune disease / unique register / experimental autoimmune encephalomyelitis / myelin basic protein
Function / homology
Function and homology information


structural constituent of myelin sheath / positive regulation of metalloendopeptidase activity / compact myelin / internode region of axon / axon ensheathment / negative regulation of heterotypic cell-cell adhesion / antigen processing and presentation of peptide antigen / EGR2 and SOX10-mediated initiation of Schwann cell myelination / membrane organization / positive regulation of chemokine (C-X-C motif) ligand 2 production ...structural constituent of myelin sheath / positive regulation of metalloendopeptidase activity / compact myelin / internode region of axon / axon ensheathment / negative regulation of heterotypic cell-cell adhesion / antigen processing and presentation of peptide antigen / EGR2 and SOX10-mediated initiation of Schwann cell myelination / membrane organization / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of T cell differentiation / maintenance of blood-brain barrier / antigen processing and presentation / negative regulation of T cell proliferation / substantia nigra development / myelination / multivesicular body / central nervous system development / cell periphery / sensory perception of sound / response to toxic substance / peptide antigen assembly with MHC class II protein complex / positive regulation of interleukin-6 production / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MAPK cascade / myelin sheath / MHC class II protein complex binding / late endosome membrane / chemical synaptic transmission / protease binding / adaptive immune response / lysosome / early endosome / calmodulin binding / immune response / lysosomal membrane / external side of plasma membrane / neuronal cell body / lipid binding / synapse / protein-containing complex binding / Golgi apparatus / cell surface / protein-containing complex / nucleus / plasma membrane / cytosol
Similarity search - Function
Myelin basic protein / Myelin basic protein / Myelin basic protein signature. / 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 ...Myelin basic protein / Myelin basic protein / Myelin basic protein signature. / 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
: / Myelin basic protein / H-2 class II histocompatibility antigen, A-U beta chain / H-2 class II histocompatibility antigen, A-U alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHe, X.L. / Radu, C. / Ward, E.S. / Garcia, K.C.
CitationJournal: IMMUNITY / Year: 2002
Title: Structural snapshot of aberrant antigen presentation linked to autoimmunity: the immunodominant epitope of MBP complexed with I-Au
Authors: He, X.L. / Radu, C. / Sidney, J. / Sette, A. / Ward, E.S. / Garcia, K.C.
History
DepositionSep 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 21, 2022Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE THE C-terminus of the MBP PEPTIDE IS LINKED TO A SYNTHETIC LINKER PEPTIDE, AND ARE Listed ...SEQUENCE THE C-terminus of the MBP PEPTIDE IS LINKED TO A SYNTHETIC LINKER PEPTIDE, AND ARE Listed in the seqres as CHAIN ID P. THE C-terminus of the LINKER PEPTIDE IS LINKED TO THE N-terminus of the BETA CHAIN. THE LINKER PEPTIDE WAS NOT SEEN IN THE ELECTRON DENSITY.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H-2 class II histocompatibility antigen, A-U alpha chain
B: H-2 class II histocompatibility antigen, A-U beta chain
P: Myelin Basic Protein peptide with 8 residue linker peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9476
Polymers46,2833
Non-polymers6643
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-20 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.150, 110.590, 94.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein H-2 class II histocompatibility antigen, A-U alpha chain / MHC CLASS II I-AU


Mass: 21468.809 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR ALPHA-1 AND ALPHA-2 DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P14438
#2: Protein H-2 class II histocompatibility antigen, A-U beta chain / MHC CLASS II I-AU


Mass: 22495.164 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR BETA-1 AND BETA-2 DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P06344
#3: Protein/peptide Myelin Basic Protein peptide with 8 residue linker peptide / MBP peptide


Mass: 2319.395 Da / Num. of mol.: 1 / Fragment: 11 residue peptide with 8 residue linker peptide / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the MBP portion of the peptide is naturally found in Homo sapiens (human).
References: GenBank: 14763906, UniProt: P02686*PLUS
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: MPEG 5000, sodium chloride, citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal grow
*PLUS
pH: 4.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG50001reservoir
250 mMammonium sulfide1reservoirpH4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 21, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 26280 / Num. obs: 26280 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3825 / % possible all: 98.7
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 144694 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 98.5 % / Rmerge(I) obs: 0.45

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IAKJ

Resolution: 2.2→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1268 4.8 %RANDOM
Rwork0.248 ---
all0.249 26276 --
obs0.249 26276 98.3 %-
Displacement parametersBiso mean: 50.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.585 Å20 Å20 Å2
2--1.876 Å2-4.462 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3105 0 42 450 3597
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.029
RfactorNum. reflection% reflection
Rfree0.354 188 -
Rwork0.323 --
obs-3244 98.5 %
Refinement
*PLUS
Highest resolution: 2.3 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4

+
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