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- PDB-3wex: Crystal structure of HLA-DP5 in complex with Cry j 1-derived pept... -

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Basic information

Entry
Database: PDB / ID: 3wex
TitleCrystal structure of HLA-DP5 in complex with Cry j 1-derived peptide (residues 214-222)
Components(MHC class II antigen) x 2
KeywordsIMMUNE SYSTEM / Immunoglobulin Fold / Antigen Presentation / T Cell Receptor / Cell Surface
Function / homology
Function and homology information


antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / endosome membrane / lysosomal 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, 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 ...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
MHC class II antigen / HLA class II histocompatibility antigen DP alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKusano, S. / Kukimoto-Niino, M. / Shirouzu, M. / Yokoyama, S.
CitationJournal: J. Mol. Biol. / Year: 2014
Title: Structural basis for the specific recognition of the major antigenic peptide from the Japanese cedar pollen allergen Cry j 1 by HLA-DP5
Authors: Kusano, S. / Kukimoto-Niino, M. / Satta, Y. / Ohsawa, N. / Uchikubo-Kamo, T. / Wakiyama, M. / Ikeda, M. / Terada, T. / Yamamoto, K. / Nishimura, Y. / Shirouzu, M. / Sasazuki, T. / Yokoyama, S.
History
DepositionJul 16, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 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_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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 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 II antigen
B: MHC class II antigen
C: MHC class II antigen
D: MHC class II antigen
E: MHC class II antigen
F: MHC class II antigen
G: MHC class II antigen
H: MHC class II antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,82412
Polymers189,9398
Non-polymers8854
Water4,810267
1
A: MHC class II antigen
B: MHC class II antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7063
Polymers47,4852
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-19 kcal/mol
Surface area18270 Å2
MethodPISA
2
C: MHC class II antigen
D: MHC class II antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7063
Polymers47,4852
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-20 kcal/mol
Surface area18580 Å2
MethodPISA
3
E: MHC class II antigen
F: MHC class II antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7063
Polymers47,4852
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-18 kcal/mol
Surface area18420 Å2
MethodPISA
4
G: MHC class II antigen
H: MHC class II antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7063
Polymers47,4852
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-21 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.150, 64.370, 130.360
Angle α, β, γ (deg.)92.99, 97.53, 109.41
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
MHC class II antigen / HLA-DP5 alpha chain


Mass: 22230.660 Da / Num. of mol.: 4 / Fragment: extracellular domain, UNP residues 32-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: baculovirus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: I2G9G1
#2: Protein
MHC class II antigen / HLA-DP5 beta chain


Mass: 25254.139 Da / Num. of mol.: 4 / Fragment: extracellular domain, UNP residues 1-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: baculovirus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: I2FL84
#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.: 4
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 24% (w/v) PEG 3350, 0.2M Ammonium nitrate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→64.28 Å / Num. obs: 70445 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.06 Å2 / Rsym value: 0.201 / Net I/σ(I): 12.31
Reflection shell
Resolution (Å)Mean I/σ(I) obsDiffraction-ID% possible all
2.4-2.572.7195.4
2.57-2.814.33195.3
2.81-3.147.58198
3.14-3.6313.18198.7
3.63-4.4420.16199
4.44-6.2622.63199.2
6.26-64.324.37199.2

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LQZ

3lqz


Resolution: 2.4→64.279 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8152 / SU ML: 0.28 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 25.93 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 3520 5 %random
Rwork0.2016 ---
obs0.2034 70389 97.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.32 Å2 / Biso mean: 29.2 Å2 / Biso min: 8.41 Å2
Refinement stepCycle: LAST / Resolution: 2.4→64.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12372 0 56 267 12695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512796
X-RAY DIFFRACTIONf_angle_d1.07117396
X-RAY DIFFRACTIONf_dihedral_angle_d14.5164664
X-RAY DIFFRACTIONf_chiral_restr0.0641848
X-RAY DIFFRACTIONf_plane_restr0.0052300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4001-2.43290.32791400.2862650279095
2.4329-2.46770.32661370.29432607274496
2.4677-2.50450.31851380.27772618275695
2.5045-2.54370.28151380.27982621275995
2.5437-2.58540.35531360.27092576271294
2.5854-2.630.28981360.27192598273495
2.63-2.67780.33531380.27132639277794
2.6778-2.72930.29731360.25622573270996
2.7293-2.7850.30141430.24362724286796
2.785-2.84560.2741390.22292629276897
2.8456-2.91170.23421410.21612695283697
2.9117-2.98460.26111400.2132645278598
2.9846-3.06530.26841440.21292736288098
3.0653-3.15550.25531400.20652675281598
3.1555-3.25730.23831440.2012721286599
3.2573-3.37370.22311430.19612713285698
3.3737-3.50880.21461410.17612697283899
3.5088-3.66850.21231430.18182706284999
3.6685-3.86180.19241440.17492740288499
3.8618-4.10380.2031440.17422730287499
4.1038-4.42050.16971420.15782701284399
4.4205-4.86530.17331440.15082735287999
4.8653-5.56890.21831440.16822739288399
5.5689-7.01490.22381430.208327082851100
7.0149-64.30190.24771420.19262693283598

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