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- PDB-4zfz: Crystal structure of rhesus macaque MHC class I molecule Mamu-B*0... -

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Basic information

Entry
Database: PDB / ID: 4zfz
TitleCrystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with myristoylated 5-mer lipopeptide derived from SIV Nef protein
Components
  • 5-mer lipopeptide from Protein Nef
  • Beta-2-microglobulinBeta-2 microglobulin
  • Major histocompatibility complex class IMHC class I
KeywordsIMMUNE SYSTEM / MHC / lipopeptide / Antigen presentation / AIDS
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation / : / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response ...virus-mediated perturbation of host defense response => GO:0019049 / antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation / : / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / membrane => GO:0016020 / immune response / lysosomal membrane / GTP binding / host cell plasma membrane / extracellular region / membrane / metal ion binding
Similarity search - Function
HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin ...HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MYRISTIC ACID / B protein / Protein Nef / Beta-2-microglobulin
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Simian immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.763 Å
AuthorsMorita, D. / Sugita, M.
CitationJournal: Nat Commun / Year: 2016
Title: Crystal structure of the N-myristoylated lipopeptide-bound MHC class I complex
Authors: Morita, D. / Yamamoto, Y. / Mizutani, T. / Ishikawa, T. / Suzuki, J. / Igarashi, T. / Mori, N. / Shiina, T. / Inoko, H. / Fujita, H. / Iwai, K. / Tanaka, Y. / Mikami, B. / Sugita, M.
History
DepositionApr 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major histocompatibility complex class I
B: Beta-2-microglobulin
C: 5-mer lipopeptide from Protein Nef
D: Major histocompatibility complex class I
E: Beta-2-microglobulin
F: 5-mer lipopeptide from Protein Nef
G: Major histocompatibility complex class I
H: Beta-2-microglobulin
I: 5-mer lipopeptide from Protein Nef
J: Major histocompatibility complex class I
K: Beta-2-microglobulin
L: 5-mer lipopeptide from Protein Nef
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,765104
Polymers175,28912
Non-polymers6,47692
Water14,592810
1
A: Major histocompatibility complex class I
B: Beta-2-microglobulin
C: 5-mer lipopeptide from Protein Nef
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,59428
Polymers43,8223
Non-polymers1,77225
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Major histocompatibility complex class I
E: Beta-2-microglobulin
F: 5-mer lipopeptide from Protein Nef
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,43125
Polymers43,8223
Non-polymers1,60922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Major histocompatibility complex class I
H: Beta-2-microglobulin
I: 5-mer lipopeptide from Protein Nef
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,27524
Polymers43,8223
Non-polymers1,45321
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Major histocompatibility complex class I
K: Beta-2-microglobulin
L: 5-mer lipopeptide from Protein Nef
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,46527
Polymers43,8223
Non-polymers1,64324
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.402, 85.179, 127.990
Angle α, β, γ (deg.)89.20, 79.57, 90.02
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 8 molecules ADGJBEHK

#1: Protein
Major histocompatibility complex class I / MHC class I


Mass: 31687.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Escherichia coli (E. coli) / References: UniProt: K4MU32*PLUS
#2: Protein
Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11731.157 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: Q6V7J5

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Protein/peptide , 1 types, 4 molecules CFIL

#3: Protein/peptide
5-mer lipopeptide from Protein Nef


Mass: 403.432 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Simian immunodeficiency virus / References: UniProt: P12482

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Non-polymers , 6 types, 902 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Zn
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 65 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 810 / 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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: Zinc chloride, Tris-HCl, PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jan 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 182504 / % possible obs: 96.2 % / Redundancy: 2.61 % / Net I/σ(I): 30.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RWJ

3rwj


Resolution: 1.763→31.18 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2284 9073 4.97 %
Rwork0.1945 --
obs0.1961 182444 95.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.763→31.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12356 0 357 810 13523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813267
X-RAY DIFFRACTIONf_angle_d1.1117904
X-RAY DIFFRACTIONf_dihedral_angle_d14.6654966
X-RAY DIFFRACTIONf_chiral_restr0.051776
X-RAY DIFFRACTIONf_plane_restr0.0062388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7627-1.78270.32122020.30384149X-RAY DIFFRACTION68
1.7827-1.80370.31952470.2855127X-RAY DIFFRACTION85
1.8037-1.82560.30242970.27415755X-RAY DIFFRACTION96
1.8256-1.84880.29722840.2745867X-RAY DIFFRACTION96
1.8488-1.87310.30223170.26355671X-RAY DIFFRACTION96
1.8731-1.89870.28253850.25675751X-RAY DIFFRACTION96
1.8987-1.92590.3043300.24875818X-RAY DIFFRACTION96
1.9259-1.95460.26873020.2235763X-RAY DIFFRACTION96
1.9546-1.98510.28983060.23225840X-RAY DIFFRACTION96
1.9851-2.01770.25913140.22155863X-RAY DIFFRACTION97
2.0177-2.05250.25562590.22745779X-RAY DIFFRACTION97
2.0525-2.08980.27153270.22665873X-RAY DIFFRACTION97
2.0898-2.130.25572870.2245879X-RAY DIFFRACTION97
2.13-2.17340.26873270.21715806X-RAY DIFFRACTION97
2.1734-2.22070.24353200.20925843X-RAY DIFFRACTION97
2.2207-2.27230.26133700.21395758X-RAY DIFFRACTION97
2.2723-2.32910.26133770.21065856X-RAY DIFFRACTION97
2.3291-2.39210.24642750.2075832X-RAY DIFFRACTION97
2.3921-2.46240.26183230.21275958X-RAY DIFFRACTION98
2.4624-2.54190.24943050.20575831X-RAY DIFFRACTION98
2.5419-2.63270.27022640.20975984X-RAY DIFFRACTION98
2.6327-2.7380.26592660.215985X-RAY DIFFRACTION98
2.738-2.86260.27822850.20765936X-RAY DIFFRACTION98
2.8626-3.01340.23053800.19775786X-RAY DIFFRACTION98
3.0134-3.2020.21872520.19176007X-RAY DIFFRACTION98
3.202-3.44890.21872800.19165917X-RAY DIFFRACTION98
3.4489-3.79550.20753120.18585963X-RAY DIFFRACTION99
3.7955-4.34340.17783100.15545945X-RAY DIFFRACTION99
4.3434-5.46750.17682390.1466030X-RAY DIFFRACTION99
5.4675-31.18540.16953310.16325799X-RAY DIFFRACTION96

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