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- PDB-6lup: Crystal structure of shark MHC CLASS I for 2.3 angstrom -

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Basic information

Entry
Database: PDB / ID: 6lup
TitleCrystal structure of shark MHC CLASS I for 2.3 angstrom
Components
  • Beta-2-microglobulin
  • MHC class I protein
  • PHE-ALA-ASN-PHE-PHE-ILE-ARG-GLY-LEU
KeywordsIMMUNE SYSTEM / MHC / SHARK / ADAPTIVE IMMUNE / PROTEIN BINDING-IMMUNE SYSTEM complex
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / MHC class I protein complex / immune response / external side of plasma membrane / extracellular space / extracellular region
Similarity search - Function
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-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 ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-2-microglobulin / MHC class I protein
Similarity search - Component
Biological speciesGinglymostoma cirratum (nurse shark)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.302 Å
AuthorsWu, Y. / Xia, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2013CB835302 China
CitationJournal: J Immunol. / Year: 2021
Title: The Structure of a Peptide-Loaded Shark MHC Class I Molecule Reveals Features of the Binding between beta 2 -Microglobulin and H Chain Conserved in Evolution.
Authors: Wu, Y. / Zhang, N. / Wei, X. / Lu, S. / Li, S. / Hashimoto, K. / Dijkstra, J.M. / Xia, C.
History
DepositionJan 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.3Nov 6, 2024Group: Structure summary / Category: 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: MHC class I protein
B: Beta-2-microglobulin
C: PHE-ALA-ASN-PHE-PHE-ILE-ARG-GLY-LEU
D: MHC class I protein
E: Beta-2-microglobulin
F: PHE-ALA-ASN-PHE-PHE-ILE-ARG-GLY-LEU


Theoretical massNumber of molelcules
Total (without water)85,5936
Polymers85,5936
Non-polymers00
Water2,882160
1
A: MHC class I protein
B: Beta-2-microglobulin
C: PHE-ALA-ASN-PHE-PHE-ILE-ARG-GLY-LEU


Theoretical massNumber of molelcules
Total (without water)42,7973
Polymers42,7973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-25 kcal/mol
Surface area18300 Å2
MethodPISA
2
D: MHC class I protein
E: Beta-2-microglobulin
F: PHE-ALA-ASN-PHE-PHE-ILE-ARG-GLY-LEU


Theoretical massNumber of molelcules
Total (without water)42,7973
Polymers42,7973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-29 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.859, 125.859, 132.473
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein MHC class I protein


Mass: 30672.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ginglymostoma cirratum (nurse shark) / Gene: Gici-UAA01 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9MX69
#2: Protein Beta-2-microglobulin


Mass: 11039.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ginglymostoma cirratum (nurse shark) / Gene: B2M, b2m / Production host: Escherichia coli (E. coli) / References: UniProt: F4ZE04
#3: Protein/peptide PHE-ALA-ASN-PHE-PHE-ILE-ARG-GLY-LEU


Mass: 1085.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.49 Å3/Da / Density % sol: 64.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: pH 7.5, 0.09 M HEPES sodium, 1.26 M Sodium citrate tribasic dihydrate,10% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 16, 2013
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 52646 / % possible obs: 99.84 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.185
Reflection shellResolution: 2.302→2.362 Å / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 4.267 / Num. unique obs: 3679 / % possible all: 99.38

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y91

5y91


Resolution: 2.302→45.622 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.272 / WRfactor Rwork: 0.246 / SU B: 0.003 / SU ML: 0 / Average fsc free: 0.8018 / Average fsc work: 0.8162 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.234
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2835 2672 5.075 %
Rwork0.2553 49974 -
all0.257 --
obs-52646 99.835 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 62.605 Å2
Baniso -1Baniso -2Baniso -3
1--0.092 Å2-0.046 Å2-0 Å2
2---0.092 Å20 Å2
3---0.299 Å2
Refinement stepCycle: LAST / Resolution: 2.302→45.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6032 0 0 160 6192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.302-2.3620.3991990.41136790.4139020.6430.63999.38490.397
2.362-2.4260.3812150.37635630.37737850.6230.63899.81510.358
2.426-2.4960.3391930.35234400.35136420.7070.71599.75290.331
2.496-2.5730.361620.33634220.33735940.6920.69499.72180.312
2.573-2.6570.3691890.32132710.32434690.70.73399.74060.296
2.657-2.750.3311620.30731410.30833080.7940.80799.84880.278
2.75-2.8530.3021400.2931070.29132490.8440.84599.93840.262
2.853-2.9690.3321550.28629520.28931100.8130.84499.90350.259
2.969-3.1010.3311420.29128420.29329850.8290.84899.96650.265
3.101-3.2510.3151640.28826910.28928560.8550.85699.9650.268
3.251-3.4260.2551400.26225770.26227170.8930.8961000.251
3.426-3.6330.2911340.24824450.25125840.8740.90199.80650.243
3.633-3.8820.2671290.24222870.24324180.8950.9199.91730.248
3.882-4.190.2381010.22321610.22422620.9270.931000.243
4.19-4.5860.256980.20519870.20720850.9170.9381000.226
4.586-5.1210.22900.18317900.18418800.9430.951000.202
5.121-5.9010.2231080.18915660.19116750.9370.95299.94030.209
5.901-7.1980.216770.213320.20114090.9360.941000.222
7.198-10.0540.172500.15710660.15811160.9610.9691000.183
10.054-45.6220.309230.1976330.26570.9090.9699.84780.242

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