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- PDB-4g59: Crystal structure of the murine cytomegalovirus MHC-I homolog m15... -

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Basic information

Entry
Database: PDB / ID: 4g59
TitleCrystal structure of the murine cytomegalovirus MHC-I homolog m152 with ligand RAE-1 gamma
Components
  • M152 protein
  • Retinoic acid early-inducible protein 1-gamma
KeywordsIMMUNE SYSTEM / MHC-I Fold / Immunoevasion / Stress induced ligand
Function / homology
Function and homology information


: / natural killer cell lectin-like receptor binding / cellular response to exogenous dsRNA / cellular response to lipopolysaccharide / membrane => GO:0016020 / defense response to bacterium / external side of plasma membrane / extracellular space
Similarity search - Function
Immunoglobulin-like - #2920 / Murid herpesvirus 1, M157 / Retinoic acid early-inducible protein 1 / MHC class I-like protein M157 / Class I Histocompatibility antigen, NKG2D ligand, domains 1 and 2 / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 - #30 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein ...Immunoglobulin-like - #2920 / Murid herpesvirus 1, M157 / Retinoic acid early-inducible protein 1 / MHC class I-like protein M157 / Class I Histocompatibility antigen, NKG2D ligand, domains 1 and 2 / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 - #30 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Retinoic acid early-inducible protein 1-gamma / M152 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Murid herpesvirus 1 (Murine cytomegalovirus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsWang, R. / Natarajan, K. / Margulies, D.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis of mouse cytomegalovirus m152/gp40 interaction with RAE1gamma reveals a paradigm for MHC/MHC interaction in immune evasion.
Authors: Wang, R. / Natarajan, K. / Revilleza, M.J. / Boyd, L.F. / Zhi, L. / Zhao, H. / Robinson, H. / Margulies, D.H.
History
DepositionJul 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jul 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_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinoic acid early-inducible protein 1-gamma
C: M152 protein
B: Retinoic acid early-inducible protein 1-gamma
D: M152 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,7298
Polymers119,8444
Non-polymers8854
Water1,35175
1
A: Retinoic acid early-inducible protein 1-gamma
C: M152 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3654
Polymers59,9222
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-1 kcal/mol
Surface area19980 Å2
MethodPISA
2
B: Retinoic acid early-inducible protein 1-gamma
D: M152 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3654
Polymers59,9222
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-1 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.443, 99.800, 68.609
Angle α, β, γ (deg.)90.00, 100.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Retinoic acid early-inducible protein 1-gamma / RAE-1-gamma


Mass: 23201.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Raet1c / Production host: Escherichia coli (E. coli) / References: UniProt: O08604
#2: Protein M152 protein


Mass: 36720.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid herpesvirus 1 (Murine cytomegalovirus)
Gene: m152 / Production host: Drosophila (fruit flies) / References: UniProt: Q83156
#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 / N-Acetylglucosamine


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 / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG3350, 0.2M KCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 29, 2010
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. all: 47756 / Num. obs: 45215 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.07
Reflection shellResolution: 2.44→2.54 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 2.8 / % possible all: 96.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBD entries 2O5N, 1JFM

2o5n

1jfm


Resolution: 2.44→47.516 Å / SU ML: 0.28 / σ(F): 1 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2451 2240 4.95 %
Rwork0.201 --
obs0.2032 45208 94.22 %
all-47756 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.8 Å2
Refinement stepCycle: LAST / Resolution: 2.44→47.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6915 0 56 75 7046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097146
X-RAY DIFFRACTIONf_angle_d1.2699672
X-RAY DIFFRACTIONf_dihedral_angle_d15.2392647
X-RAY DIFFRACTIONf_chiral_restr0.0851042
X-RAY DIFFRACTIONf_plane_restr0.0051250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.48950.2913950.27622220X-RAY DIFFRACTION78
2.4895-2.54740.29231240.2552470X-RAY DIFFRACTION86
2.5474-2.61110.32941220.25622509X-RAY DIFFRACTION89
2.6111-2.68170.28021550.24272556X-RAY DIFFRACTION91
2.6817-2.76060.30151210.23952635X-RAY DIFFRACTION92
2.7606-2.84970.32161550.23792641X-RAY DIFFRACTION94
2.8497-2.95160.27751330.24072723X-RAY DIFFRACTION96
2.9516-3.06970.3091360.25052715X-RAY DIFFRACTION96
3.0697-3.20940.2851500.23622764X-RAY DIFFRACTION97
3.2094-3.37860.26851390.21522761X-RAY DIFFRACTION97
3.3786-3.59020.28221570.21422784X-RAY DIFFRACTION98
3.5902-3.86730.22441430.19252818X-RAY DIFFRACTION99
3.8673-4.25620.22611480.16992818X-RAY DIFFRACTION99
4.2562-4.87160.18781520.15282823X-RAY DIFFRACTION99
4.8716-6.13560.221590.18222833X-RAY DIFFRACTION99
6.1356-47.5250.21011510.18412898X-RAY DIFFRACTION99

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