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- PDB-3c6l: Crystal structure of mouse MHC class II I-Ab/3K peptide complexed... -

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Basic information

Entry
Database: PDB / ID: 3c6l
TitleCrystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR 2W20
Components
  • 3K peptide, Linker,and H-2 class II histocompatibility antigen (A beta chain)
  • H-2 class II histocompatibility antigen, A-B alpha chain
  • TCR 2W20 alpha chain
  • TCR 2W20 beta chain
KeywordsSUGAR BINDING PROTEIN/IMMUNE SYSTEM / TCR-pMHC complex / Glycoprotein / Immune response / Membrane / MHC II / Transmembrane / SUGAR BINDING PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / protein antigen binding / antigen processing and presentation of peptide antigen / B cell affinity maturation / positive regulation of T cell differentiation / response to type II interferon / antigen processing and presentation / toxic substance binding ...positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / protein antigen binding / antigen processing and presentation of peptide antigen / B cell affinity maturation / positive regulation of T cell differentiation / response to type II interferon / antigen processing and presentation / toxic substance binding / negative regulation of T cell proliferation / multivesicular body / 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 / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / lysosome / early endosome / immune response / lysosomal membrane / external side of plasma membrane / ubiquitin protein ligase binding / protein-containing complex binding / Golgi apparatus / cell surface / 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
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å
AuthorsDai, S.
CitationJournal: Immunity / Year: 2008
Title: Crossreactive T Cells spotlight the germline rules for alphabeta T cell-receptor interactions with MHC molecules.
Authors: Dai, S. / Huseby, E.S. / Rubtsova, K. / Scott-Browne, J. / Crawford, F. / Macdonald, W.A. / Marrack, P. / Kappler, J.W.
History
DepositionFeb 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software / Item: _software.classification
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TCR 2W20 alpha chain
B: TCR 2W20 beta chain
C: H-2 class II histocompatibility antigen, A-B alpha chain
D: 3K peptide, Linker,and H-2 class II histocompatibility antigen (A beta chain)
E: TCR 2W20 alpha chain
F: TCR 2W20 beta chain
G: H-2 class II histocompatibility antigen, A-B alpha chain
H: 3K peptide, Linker,and H-2 class II histocompatibility antigen (A beta chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,08311
Polymers185,9638
Non-polymers1203
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.540, 113.930, 386.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TCR 2W20 alpha chain


Mass: 20957.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
#2: Protein TCR 2W20 beta chain


Mass: 26487.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
#3: Protein H-2 class II histocompatibility antigen, A-B alpha chain / IAalpha


Mass: 20597.957 Da / Num. of mol.: 2 / Fragment: UNP residues 27-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P14434
#4: Protein 3K peptide, Linker,and H-2 class II histocompatibility antigen (A beta chain)


Mass: 24938.830 Da / Num. of mol.: 2
Fragment: Fusion protein of Ealpha3K peptide residues 1-13, linker 14-28 and MHC class II Ab UNP residues 30-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Ab1, H2-iabeta / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P14483
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
Sequence detailsIN A RELATED ENTRY 1LNU, AUTHORS STATED TWO SEPARATE SEQUENCES, AN EALPHA3KPEPTIDE(1-13), AND ...IN A RELATED ENTRY 1LNU, AUTHORS STATED TWO SEPARATE SEQUENCES, AN EALPHA3KPEPTIDE(1-13), AND LINKER(14-28), WHICH START FROM RESIDUE 1 TO RESIDUE 28 WERE ADDED TO THE N-TERMINUS OF THE BETACHAIN OF THE CLASS II MHC IAB OF CHAINS D AND H

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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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 16% PEG 4000, 100mM calcium acetate, pH 6.0, 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: Apr 9, 2007 / 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
ReflectionRedundancy: 5.4 % / Av σ(I) over netI: 8 / Number: 157260 / Rmerge(I) obs: 0.131 / Χ2: 1.65 / D res high: 3.4 Å / D res low: 50 Å / Num. obs: 28945 / % possible obs: 97.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.325099.110.0371.9235.4
5.817.3298.410.0831.7085.3
5.085.8198.110.1061.8565.4
4.615.0898.610.111.7895.5
4.284.6198.810.1361.5955.5
4.034.2899.110.2341.545.6
3.834.0399.310.4011.4865.5
3.663.839910.5311.5665.6
3.523.669610.7071.5195.4
3.43.5289.510.7691.4445.1
ReflectionResolution: 3.4→50 Å / Num. obs: 28945 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.131 / Χ2: 1.649 / Net I/σ(I): 14.4
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.769 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2613 / Χ2: 1.444 / % possible all: 89.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNS1.1refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
HKL-3000data reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→49.07 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 4521952 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.325 1425 4.9 %RANDOM
Rwork0.268 ---
obs-28844 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.886 Å2 / ksol: 0.283 e/Å3
Displacement parametersBiso mean: 95.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.64 Å20 Å20 Å2
2--19.01 Å20 Å2
3----16.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.83 Å0.74 Å
Refinement stepCycle: LAST / Resolution: 3.4→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12714 0 3 0 12717
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.4→3.61 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.406 225 5 %
Rwork0.348 4238 -
all-4463 -
obs-4238 92.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2carbohydrate.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3water_rep.param&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4ion.param&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5ioh.par&_1_TOPOLOGY_INFILE_5

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