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- PDB-1iak: HISTOCOMPATIBILITY ANTIGEN I-AK -

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Basic information

Entry
Database: PDB / ID: 1iak
TitleHISTOCOMPATIBILITY ANTIGEN I-AK
Components(MHC CLASS II I-AK) x 3
KeywordsHISTOCOMPATIBILITY ANTIGEN I-AK / HISTOCOMPATIBILITY ANTIGEN / MHC / PEPTIDE COMPLEX
Function / homology
Function and homology information


Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / Downstream TCR signaling / cytolysis / antigen processing and presentation of peptide antigen / MHC class II antigen presentation / positive regulation of T cell differentiation / antigen processing and presentation ...Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / Downstream TCR signaling / cytolysis / antigen processing and presentation of peptide antigen / MHC class II antigen presentation / positive regulation of T cell differentiation / antigen processing and presentation / metabolic process / negative regulation of T cell proliferation / multivesicular body / 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 / lysozyme / MHC class II protein complex binding / late endosome membrane / lysozyme activity / adaptive immune response / lysosome / early endosome / defense response to bacterium / immune response / lysosomal membrane / external side of plasma membrane / protein-containing complex binding / Golgi apparatus / cell surface / extracellular region / membrane / plasma membrane
Similarity search - Function
Lysozyme C / 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 ...Lysozyme C / 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 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / MHC classes I/II-like antigen recognition protein / Lysozyme-like domain superfamily / 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-K alpha chain / H-2 class II histocompatibility antigen, A-K beta chain / Lysozyme C / Lysozyme
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFremont, D.H. / Unanue, E.R. / Hendrickson, W.A.
CitationJournal: Immunity / Year: 1998
Title: Crystal structure of I-Ak in complex with a dominant epitope of lysozyme.
Authors: Fremont, D.H. / Monnaie, D. / Nelson, C.A. / Hendrickson, W.A. / Unanue, E.R.
History
DepositionNov 18, 1997Processing site: BNL
Revision 1.0Apr 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / software / 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 / _software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC CLASS II I-AK
B: MHC CLASS II I-AK
P: MHC CLASS II I-AK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7946
Polymers46,1313
Non-polymers6643
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-23 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.250, 112.250, 99.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-191-

HOH

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Components

#1: Protein MHC CLASS II I-AK


Mass: 22689.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: WITH COVALENTLY BOUND HEL PEPTIDE / Source: (gene. exp.) Mus musculus (house mouse) / Cell line: CHO / Organ: EGG / Production host: CHO CELLS AS GPI-LINKED PROTEIN / References: UniProt: P01910
#2: Protein MHC CLASS II I-AK


Mass: 21887.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: WITH COVALENTLY BOUND HEL PEPTIDE / Source: (gene. exp.) Mus musculus (house mouse) / Cell line: CHO / Organ: EGG / Production host: CHO CELLS AS GPI-LINKED PROTEIN / References: UniProt: P06343
#3: Protein/peptide MHC CLASS II I-AK


Mass: 1553.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: WITH COVALENTLY BOUND HEL PEPTIDE / Source: (gene. exp.) Mus musculus (house mouse) / Production host: CHO CELLS AS GPI-LINKED PROTEIN / References: UniProt: P24364, UniProt: Q29431*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


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


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS ENTRY CONTAINS COORDINATES FOR THE EXTRACELLULAR DOMAINS OF THE MURINE MHC CLASS II MOLECULE I- ...THIS ENTRY CONTAINS COORDINATES FOR THE EXTRACELLULAR DOMAINS OF THE MURINE MHC CLASS II MOLECULE I-AK WITH A. PEPTIDE FROM HEN EGG WHITE LYSOZYME (50 - 62) COVALENTLY ATTACHED TO THE I-AK BETA CHAIN VIA A POLYPEPTIDE LINKER. THE HETERODIMER WAS EXPRESSED IN CHO CELLS AS A GPI-LINKED PROTEIN AND ENZYMATICALLY CLEAVED WITH PIPLC. FOR THE I-AK ALPHA CHAIN, THE FIRST 3 RESIDUES AND LAST 14 RESIDUES COULD NOT BE TRACED. FOR THE BETA CHAIN, 10 RESIDUES AMINO TERMINAL TO THE HEL PEPTIDE AND 16 RESIDUES IN THE COVALENT LINKER WERE DISORDERED, AS WERE 15 RESIDUES AT THE C-TERMINAL TAIL OF THE BETA CHAIN. THE FIRST TWO RESIDUES BUILT IN THE BETA CHAIN (GLY B5 AND SER B6) ARE IN FACT CLONING ARTIFACTS OF THE LINKER CONSTRUCTION, AS THESE RESIDUES ARE ARG B5 AND HIS B6 IN THE NATURAL I-AK SEQUENCE. THE HETEROATOM WATER 1 SITS AT A SPECIAL POSITION. ALL OTHER WATERS ARE NUMBERED IN ORDER OF THEIR TEMPERATURE FACTOR. HEL PEPTIDE RESIDUES 50-62 CORRESPOND TO BINDING SITES P-2 TO P11.

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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: 3.4 Å3/Da / Density % sol: 63.85 %
Crystal growpH: 4.75
Details: 20% PEG 4000, 7% EG, 80MM A.S, 200MM AMM.ACETATE, 50MM NA.ACETATE PH 4.75
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 %PEG1reservoir
37 %ethylene glycol1reservoir
480 mMammonium sulfate1reservoir
5200 mMammonium acetate1reservoir
650 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9763
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 48139 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 4.12 % / Biso Wilson estimate: 25.1 Å2 / Rsym value: 0.05 / Net I/σ(I): 11.7
Reflection shellResolution: 1.9→1.99 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.27 / % possible all: 96.6
Reflection
*PLUS
Num. measured all: 198306 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 96.6 % / Rmerge(I) obs: 0.27

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Processing

Software
NameVersionClassification
HKLdata collection
DENZOdata reduction
SCALAdata scaling
Agrovatadata reduction
X-PLORmodel building
X-PLORrefinement
HKLdata reduction
CCP4(AGROVATAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IEA

1iea


Resolution: 1.9→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2410 5 %RANDOM
Rwork0.214 ---
obs0.214 47865 95.7 %-
Displacement parametersBiso mean: 30.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.22 Å20 Å20 Å2
2---4.22 Å20 Å2
3---8.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-10 Å
Luzzati sigma a0.32 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3129 0 42 369 3540
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.18
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.471.5
X-RAY DIFFRACTIONx_mcangle_it2.532
X-RAY DIFFRACTIONx_scbond_it1.652
X-RAY DIFFRACTIONx_scangle_it2.672.5
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.392 293 4.9 %
Rwork0.357 5627 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3_MOD.CHOTOPH3.CHO
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.18
LS refinement shell
*PLUS
Rfactor obs: 0.357

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