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- PDB-1fng: HISTOCOMPATIBILITY ANTIGEN -

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Basic information

Entry
Database: PDB / ID: 1fng
TitleHISTOCOMPATIBILITY ANTIGEN
Components
  • PROTEIN (MHC CLASS II I-EK, ALPHA CHAIN)
  • PROTEIN (MHC CLASS II I-EK, BETA CHAIN)
KeywordsIMMUNE SYSTEM / HISTOCOMPATIBILITY ANTIGEN / MHC
Function / homology
Function and homology information


positive regulation of myeloid cell differentiation / myeloid cell differentiation / nitric oxide transport / hemoglobin complex / oxygen transport / immunoglobulin mediated immune response / erythrocyte development / oxygen carrier activity / peptide antigen assembly with MHC class II protein complex / carbon dioxide transport ...positive regulation of myeloid cell differentiation / myeloid cell differentiation / nitric oxide transport / hemoglobin complex / oxygen transport / immunoglobulin mediated immune response / erythrocyte development / oxygen carrier activity / peptide antigen assembly with MHC class II protein complex / carbon dioxide transport / MHC class II protein complex / regulation of erythrocyte differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class II / oxygen binding / positive regulation of immune response / peptide antigen binding / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / lysosome / external side of plasma membrane / lysosomal membrane / heme binding / metal ion binding / 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 / 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 / Hemoglobin, beta-type / : / Globin/Protoglobin ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / 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 / Hemoglobin, beta-type / : / Globin/Protoglobin / Globin domain profile. / Globin / Globin / Globin-like superfamily / 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
: / Hemoglobin subunit beta-2 / H-2 class II histocompatibility antigen, E-K alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsMiley, M.J. / Nelson, C.A. / Fremont, D.H.
CitationJournal: J.Immunol. / Year: 2001
Title: Structural and functional consequences of altering a peptide MHC anchor residue.
Authors: Kersh, G.J. / Miley, M.J. / Nelson, C.A. / Grakoui, A. / Horvath, S. / Donermeyer, D.L. / Kappler, J. / Allen, P.M. / Fremont, D.H.
History
DepositionAug 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 23, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_residues / software
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Nov 20, 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_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (MHC CLASS II I-EK, ALPHA CHAIN)
B: PROTEIN (MHC CLASS II I-EK, BETA CHAIN)
C: PROTEIN (MHC CLASS II I-EK, ALPHA CHAIN)
D: PROTEIN (MHC CLASS II I-EK, BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,80210
Polymers95,4754
Non-polymers1,3276
Water9,134507
1
A: PROTEIN (MHC CLASS II I-EK, ALPHA CHAIN)
B: PROTEIN (MHC CLASS II I-EK, BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4015
Polymers47,7372
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-29 kcal/mol
Surface area19370 Å2
MethodPISA
2
C: PROTEIN (MHC CLASS II I-EK, ALPHA CHAIN)
D: PROTEIN (MHC CLASS II I-EK, BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4015
Polymers47,7372
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-30 kcal/mol
Surface area19250 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17090 Å2
ΔGint-49 kcal/mol
Surface area35570 Å2
MethodPISA
4
A: PROTEIN (MHC CLASS II I-EK, ALPHA CHAIN)
B: PROTEIN (MHC CLASS II I-EK, BETA CHAIN)
C: PROTEIN (MHC CLASS II I-EK, ALPHA CHAIN)
D: PROTEIN (MHC CLASS II I-EK, BETA CHAIN)
hetero molecules

A: PROTEIN (MHC CLASS II I-EK, ALPHA CHAIN)
B: PROTEIN (MHC CLASS II I-EK, BETA CHAIN)
C: PROTEIN (MHC CLASS II I-EK, ALPHA CHAIN)
D: PROTEIN (MHC CLASS II I-EK, BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,60420
Polymers190,9498
Non-polymers2,65412
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)147.140, 57.024, 116.809
Angle α, β, γ (deg.)90.00, 91.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-634-

HOH

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Components

#1: Protein PROTEIN (MHC CLASS II I-EK, ALPHA CHAIN)


Mass: 22361.051 Da / Num. of mol.: 2 / Fragment: SOLUBLE ECTO-DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04224
#2: Protein PROTEIN (MHC CLASS II I-EK, BETA CHAIN)


Mass: 25376.279 Da / Num. of mol.: 2
Fragment: SOLUBLE ECTO-DOMAIN PLUS COVALENTLY ATTACHED HB PEPTIDE
Source method: isolated from a genetically manipulated source
Details: WITH COVALENTLY BOUND HB PEPTIDE / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P02089, GenBank: AAA39594
#3: 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.: 6 / Source method: obtained synthetically / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / 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-EK WITH A PEPTIDE FROM MURINE HEMOGLOBIN (64 - 76) COVALENTLY ATTACHED TO THE I-EK BETA CHAIN VIA A POLYPEPTIDE LINKER. NO ATTEMPT WAS MADE TO MODEL FIVE RESIDUES AMINO TERMINAL TO THE BETA CHAIN OR TEN RESIDUES CARBOXY TERMINAL TO EITHER THE ALPHA OR BETA CHAINS. RESIDUES 105-113 IN THE B AND D CHAINS HAVE OCCUPANCIES SET TO ZERO DUE TO LACK OF COHERENT ELECTRON DENSITY.THERE ARE TWO HETERODIMERS IN THE ASYMMETRIC UNIT RELATED BY AN APPROXIMATE TWO-FOLD AXIS.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 15% PEG 4000 15% 2-PROPANOL 300mM-500mM AMMONIUM ACETATE 100mM CITRATE PH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 OD280protein1drop
210 mMHEPES1drop
35 mMsodium azide1drop
415 %PEG40001reservoir
515 %2-propanol1reservoir
6300-500 mMammonium acetate1reservoir
7100 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. all: 445426 / Num. obs: 76496 / % possible obs: 98.6 % / Redundancy: 5.82 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 19.8
Reflection shellResolution: 1.9→1.96 Å / Rmerge(I) obs: 0.296 / % possible all: 75.4
Reflection
*PLUS
Num. measured all: 445426
Reflection shell
*PLUS
% possible obs: 92.6 % / Mean I/σ(I) obs: 3.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 1.9→19.78 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 865351.58 / Data cutoff high rms absF: 73492 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.254 3647 5 %RANDOM
Rwork0.221 ---
obs0.221 73492 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.63 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso mean: 37.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.4 Å20 Å2-2.24 Å2
2--10.04 Å20 Å2
3----4.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6422 0 84 507 7013
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.22
X-RAY DIFFRACTIONc_scbond_it1.72
X-RAY DIFFRACTIONc_scangle_it2.642.5
LS refinement shellResolution: 1.9→1.96 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.32 240 4.4 %
Rwork0.298 5231 -
obs--86.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PCARBOHYDRATE.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.32 / % reflection Rfree: 4.4 % / Rfactor Rwork: 0.298 / Rfactor obs: 0.296

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