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- PDB-1muj: Crystal structure of murine class II MHC I-Ab in complex with a h... -

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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 / macrophage migration inhibitory factor binding / negative regulation of T cell differentiation ...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 / macrophage migration inhibitory factor binding / negative regulation of T cell differentiation / 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 / positive regulation of prostaglandin biosynthetic process / T cell activation involved in immune response / T cell selection / positive regulation of type 2 immune response / antigen processing and presentation of peptide antigen / B cell affinity maturation / host-mediated suppression of symbiont invasion / negative thymic T cell selection / MHC class II protein binding / negative regulation of mature B cell apoptotic process / positive regulation of kinase activity / protein antigen binding / positive regulation of monocyte differentiation / positive thymic T cell selection / vacuole / CD4 receptor binding / cytokine receptor activity / positive regulation of neutrophil chemotaxis / positive regulation of chemokine (C-X-C motif) ligand 2 production / prostaglandin biosynthetic process / positive regulation of macrophage cytokine production / positive regulation of T cell differentiation / transport vesicle membrane / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of macrophage activation / antigen processing and presentation / cytokine binding / nitric-oxide synthase binding / negative regulation of DNA damage response, signal transduction by p53 class mediator / : / immunoglobulin mediated immune response / response to type II interferon / toxic substance binding / positive regulation of chemokine production / positive regulation of B cell proliferation / multivesicular body / protein folding chaperone / MHC class II antigen presentation / lysosomal lumen / negative regulation of cell migration / trans-Golgi network membrane / Cell surface interactions at the vascular wall / positive regulation of interleukin-8 production / lumenal side of endoplasmic reticulum membrane / intracellular protein transport / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / cellular response to type II interferon / positive regulation of interleukin-6 production / positive regulation of protein phosphorylation / positive regulation of fibroblast proliferation / MHC class II protein complex binding / endocytic vesicle membrane / late endosome / amyloid-beta binding / protein-containing complex assembly / adaptive immune response / positive regulation of viral entry into host cell / early endosome / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / protein stabilization / immune response / Golgi membrane / lysosomal membrane / external side of plasma membrane / ubiquitin protein ligase binding / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / Golgi apparatus / protein-containing complex / extracellular exosome / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm
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 ...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 / Roll / Immunoglobulin-like fold / Immunoglobulins / 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
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
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: 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

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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 / 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.: 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
Has protein modificationY

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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: 2.42 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

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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

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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

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