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- PDB-1a6a: THE STRUCTURE OF AN INTERMEDIATE IN CLASS II MHC MATURATION: CLIP... -

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Entry
Database: PDB / ID: 1a6a
TitleTHE STRUCTURE OF AN INTERMEDIATE IN CLASS II MHC MATURATION: CLIP BOUND TO HLA-DR3
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DR-1 beta chain
  • HLA class II histocompatibility antigen, gamma chain
KeywordsCOMPLEX (TRANSMEMBRANE/GLYCOPROTEIN) / MHC GLYCOPROTEIN / COMPLEX (TRANSMEMBRANE-GLYCOPROTEIN) / COMPLEX (TRANSMEMBRANE-GLYCOPROTEIN) complex
Function / homology
Function and homology information


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 ...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 / regulation of interleukin-4 production / positive regulation of cytokine-mediated signaling pathway / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of prostaglandin biosynthetic process / T cell activation involved in immune response / T cell selection / positive regulation of type 2 immune response / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / host-mediated suppression of symbiont invasion / positive regulation of CD4-positive, alpha-beta T cell activation / negative thymic T cell selection / MHC class II protein binding / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / negative regulation of mature B cell apoptotic process / positive regulation of T cell mediated immune response to tumor cell / positive regulation of kinase activity / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / positive thymic T cell selection / inflammatory response to antigenic stimulus / vacuole / CD4 receptor binding / cytokine receptor activity / positive regulation of neutrophil chemotaxis / positive regulation of chemokine (C-X-C motif) ligand 2 production / intermediate filament / prostaglandin biosynthetic process / positive regulation of macrophage cytokine production / T-helper 1 type immune response / positive regulation of T cell differentiation / transport vesicle membrane / regulation of macrophage activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / antigen processing and presentation / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / nitric-oxide synthase binding / cytokine binding / negative regulation of DNA damage response, signal transduction by p53 class mediator / polysaccharide binding / negative regulation of type II interferon production / : / immunoglobulin mediated immune response / humoral immune response / macrophage differentiation / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / epidermis development / response to type II interferon / positive regulation of insulin secretion involved in cellular response to glucose stimulus / detection of bacterium / T cell receptor binding / positive regulation of chemokine production / negative regulation of T cell proliferation / 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 / protein tetramerization / peptide antigen assembly with MHC class II protein complex / intracellular protein transport / negative regulation of inflammatory response to antigenic stimulus / 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 / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / structural constituent of cytoskeleton / positive regulation of interleukin-6 production / positive regulation of T cell mediated cytotoxicity / cognition / positive regulation of protein phosphorylation / positive regulation of fibroblast proliferation / Interferon gamma signaling / MHC class II protein complex binding
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, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen gamma chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsGhosh, P. / Amaya, M. / Mellins, E. / Wiley, D.C.
CitationJournal: Nature / Year: 1995
Title: The structure of an intermediate in class II MHC maturation: CLIP bound to HLA-DR3.
Authors: Ghosh, P. / Amaya, M. / Mellins, E. / Wiley, D.C.
History
DepositionFeb 22, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / software / struct_conn / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 2, 2023Group: Advisory / Database references ...Advisory / Database references / Refinement description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DR-1 beta chain
C: HLA class II histocompatibility antigen, gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5235
Polymers44,0813
Non-polymers4422
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-42 kcal/mol
Surface area17990 Å2
MethodPISA
2
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DR-1 beta chain
C: HLA class II histocompatibility antigen, gamma chain
hetero molecules

A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DR-1 beta chain
C: HLA class II histocompatibility antigen, gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,04610
Polymers88,1616
Non-polymers8854
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area17000 Å2
ΔGint-85 kcal/mol
Surface area33650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.450, 78.450, 159.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein HLA class II histocompatibility antigen, DR alpha chain


Mass: 20469.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: B-LYMPHOCYTE / Cell line: 9.5.3 / Cellular location: PLASMA MEMBRANE / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DR-1 beta chain


Mass: 21935.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: B-LYMPHOCYTE / Cell line: 9.5.3 / Cellular location: PLASMA MEMBRANE / References: UniProt: P01912, UniProt: P01911*PLUS
#3: Protein/peptide HLA class II histocompatibility antigen, gamma chain


Mass: 1676.118 Da / Num. of mol.: 1 / Fragment: CLIP FRAGMENT 87 - 101 OF INVARIANT CHAIN / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: B-LYMPHOCYTE / Cell line: 9.5.3 / Cellular location: PLASMA MEMBRANE / References: UniProt: P04233
#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.: 22 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 52 %
Crystal growpH: 4.5
Details: 12% PEG 4K, 100 MM MGCL2, 100 MM ACETATE BUFFER, PH 4.5
Crystal grow
*PLUS
Method: unknown
Details: conditions similar to: Gorga, J.C., (1991) Res. Immun., 142, 401.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 %PEG400011
2100 mM11MgCl2
3100 mMacetate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jul 1, 1994 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.75→15 Å / Num. obs: 14428 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 6.7
Reflection shellResolution: 2.75→3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.3 / % possible all: 97.2
Reflection
*PLUS
Num. obs: 13021
Reflection shell
*PLUS
% possible obs: 97.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
ROTAVATA/AGROVATAdata reduction
AMoREphasing
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DLH

1dlh


Resolution: 2.75→6 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 5 - 180 OF THE ALPHA SUBUNIT AND RESIDUES 5 - 191 OF THE BETA SUBUNIT ARE CLEARLY VISIBLE IN 2FO-FC ELECTRON DENSITY MAPS. THREE SMALL BREAKS IN MAIN-CHAIN DENSITY OCCUR IN LOOP ...Details: RESIDUES 5 - 180 OF THE ALPHA SUBUNIT AND RESIDUES 5 - 191 OF THE BETA SUBUNIT ARE CLEARLY VISIBLE IN 2FO-FC ELECTRON DENSITY MAPS. THREE SMALL BREAKS IN MAIN-CHAIN DENSITY OCCUR IN LOOP REGIONS OF THE BETA 2 DOMAIN (AT BETA 109, 172, AND 189).
RfactorNum. reflection% reflectionSelection details
Rfree0.325 1323 10.1 %RANDOM
Rwork0.246 ---
obs0.246 13095 97.9 %-
Displacement parametersBiso mean: 47.6 Å2
Baniso -1Baniso -2Baniso -3
1--10 Å2-10 Å20 Å2
2---10 Å20 Å2
3---10 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.72 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 2.75→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3108 0 28 22 3158
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.31
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.533
X-RAY DIFFRACTIONx_mcangle_it5.984
X-RAY DIFFRACTIONx_scbond_it5.524
X-RAY DIFFRACTIONx_scangle_it9.356
LS refinement shellResolution: 2.75→2.86 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.444 162 10.1 %
Rwork0.373 1442 -
obs--96.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM3_MOD.CHOTOPH3.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.31
LS refinement shell
*PLUS
Rfactor obs: 0.373

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