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- PDB-1fne: HISTOCOMPATIBILITY ANTIGEN -

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Basic information

Entry
Database: PDB / ID: 1fne
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 / erythrocyte development / hemoglobin complex / immunoglobulin mediated immune response / oxygen transport / 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 / erythrocyte development / hemoglobin complex / immunoglobulin mediated immune response / oxygen transport / oxygen carrier activity / peptide antigen assembly with MHC class II protein complex / carbon dioxide transport / MHC class II protein complex / regulation of erythrocyte differentiation / oxygen binding / 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 / MHC class II protein complex binding / late endosome membrane / lysosome / lysosomal membrane / external side of plasma 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 / 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 ...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, 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 / Globin / Globin domain profile. / 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 / MOLECULAR REPLACEMENT / 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 1.3Aug 23, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Aug 9, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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)96,77410
Polymers95,4474
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)48,3875
Polymers47,7232
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-28 kcal/mol
Surface area19310 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)48,3875
Polymers47,7232
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-29 kcal/mol
Surface area19300 Å2
MethodPISA
3
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)193,54820
Polymers190,8938
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)146.900, 56.853, 116.726
Angle α, β, γ (deg.)90.00, 91.76, 90.00
Int Tables number5
Space group name H-MC121

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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: 25362.254 Da / Num. of mol.: 2
Fragment: SOLUBLE ECTO-DOMAIN WITH COVALENTLY ATTACHED HB PEPTIDE
Mutation: E(6P)D IN PEPTIDE RESIDUE 6P
Source method: isolated from a genetically manipulated source
Details: WITH COVALENTLY BOUND HB(D73) 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 MODIFIED 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
Sequence detailsRESIDUES (1L - 16L)IN CHAINS B & D FORM A POLYPEPTIDE LINKER REGION

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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: 2.55 Å3/Da / Density % sol: 51.78 %
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: 364002 / Num. obs: 72521 / % possible obs: 94.4 % / Redundancy: 5.01 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 13.5
Reflection shellResolution: 1.9→1.96 Å / Rmerge(I) obs: 0.301 / % possible all: 92.6
Reflection
*PLUS
Num. measured all: 364002
Reflection shell
*PLUS
% possible obs: 75.6 % / Mean I/σ(I) obs: 2.45

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IEA

1iea


Resolution: 1.9→19.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 845534.75 / Data cutoff high rms absF: 845534.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27 3604 5.1 %RANDOM
Rwork0.231 ---
obs0.231 70818 92.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.25 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 41.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.84 Å20 Å2-4.32 Å2
2--10.91 Å20 Å2
3----5.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6420 0 84 507 7011
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_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_scangle_it2.782.5
LS refinement shellResolution: 1.9→1.96 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.42 243 5 %
Rwork0.36 4616 -
obs--76.9 %
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: 5.1 % / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41.4 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_deg0.83
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: 0.42 / % reflection Rfree: 5 % / Rfactor Rwork: 0.36 / Rfactor obs: 0.36

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