[English] 日本語
Yorodumi
- PDB-4hkj: Structure of Cowpox CPXV203 in complex with MHCI (H-2Kb) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hkj
TitleStructure of Cowpox CPXV203 in complex with MHCI (H-2Kb)
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • CPXV203 protein
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • Ovalbumin
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / viral immune evasion proteins / antigen presentation / structural genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / inhibitor / intracellular / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib ...intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / response to steroid hormone / embryo development ending in birth or egg hatching / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / negative regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / response to corticosterone / positive regulation of natural killer cell mediated cytotoxicity / inner ear development / positive regulation of natural killer cell proliferation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / MHC class I protein binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / phagocytic vesicle / monoatomic ion transport / TAP binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / response to progesterone / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / response to estrogen / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
Similarity search - Function
Viral Chemokine Inhibitor; Chain A - #30 / Poxvirus T4 protein, C-terminal / Poxvirus T4 protein, N-terminal / Apoptosis regulator, M-T4, endoplasmic reticulum / Apoptosis regulator, M-T4 superfamily / Poxvirus T4 protein, C terminus / Poxvirus T4 protein, N terminus / Viral Chemokine Inhibitor; Chain A / Serpin, conserved site / Serpins signature. ...Viral Chemokine Inhibitor; Chain A - #30 / Poxvirus T4 protein, C-terminal / Poxvirus T4 protein, N-terminal / Apoptosis regulator, M-T4, endoplasmic reticulum / Apoptosis regulator, M-T4 superfamily / Poxvirus T4 protein, C terminus / Poxvirus T4 protein, N terminus / Viral Chemokine Inhibitor; Chain A / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / 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
Ovalbumin / H-2 class I histocompatibility antigen, K-B alpha chain / Beta-2-microglobulin / CPXV203 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
Cowpox virus
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 3 Å
AuthorsMcCoy IV, W.H. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Plos Biol. / Year: 2012
Title: Structural Mechanism of ER Retrieval of MHC Class I by Cowpox.
Authors: McCoy, W.H. / Wang, X. / Yokoyama, W.M. / Hansen, T.H. / Fremont, D.H.
History
DepositionOct 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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 / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
C: Ovalbumin
D: CPXV203 protein
E: H-2 class I histocompatibility antigen, K-B alpha chain
F: Beta-2-microglobulin
G: Ovalbumin
H: CPXV203 protein
I: H-2 class I histocompatibility antigen, K-B alpha chain
J: Beta-2-microglobulin
K: Ovalbumin
L: CPXV203 protein
M: H-2 class I histocompatibility antigen, K-B alpha chain
N: Beta-2-microglobulin
O: Ovalbumin
P: CPXV203 protein


Theoretical massNumber of molelcules
Total (without water)275,98716
Polymers275,98716
Non-polymers00
Water1,29772
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
C: Ovalbumin
D: CPXV203 protein


Theoretical massNumber of molelcules
Total (without water)68,9974
Polymers68,9974
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-28 kcal/mol
Surface area27310 Å2
MethodPISA
2
E: H-2 class I histocompatibility antigen, K-B alpha chain
F: Beta-2-microglobulin
G: Ovalbumin
H: CPXV203 protein


Theoretical massNumber of molelcules
Total (without water)68,9974
Polymers68,9974
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-27 kcal/mol
Surface area27360 Å2
MethodPISA
3
I: H-2 class I histocompatibility antigen, K-B alpha chain
J: Beta-2-microglobulin
K: Ovalbumin
L: CPXV203 protein


Theoretical massNumber of molelcules
Total (without water)68,9974
Polymers68,9974
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-28 kcal/mol
Surface area27340 Å2
MethodPISA
4
M: H-2 class I histocompatibility antigen, K-B alpha chain
N: Beta-2-microglobulin
O: Ovalbumin
P: CPXV203 protein


Theoretical massNumber of molelcules
Total (without water)68,9974
Polymers68,9974
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-28 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.31, 88.25, 106.42
Angle α, β, γ (deg.)76.18, 69.29, 66.69
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 1:277 )
21chain E and (resseq 1:277 )
31chain I and (resseq 1:277 )
41chain M and (resseq 1:277 )
12chain D and (resseq 5:190 )
22chain H and (resseq 5:190 )
32chain L and (resseq 5:190 )
42chain P and (resseq 5:190 )
13chain B and (resseq 0:99 )
23chain F and (resseq 0:99 )
33chain J and (resseq 0:99 )
43chain N and (resseq 0:99 )
14chain C and (resseq 1:8 )
24chain G and (resseq 1:8 )
34chain K and (resseq 1:8 )
44chain O and (resseq 1:8 )

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROchain 'A' and (resseq 1:277 )AA1 - 2771 - 277
21GLYGLYPROPROchain 'E' and (resseq 1:277 )EE1 - 2771 - 277
31GLYGLYPROPROchain 'I' and (resseq 1:277 )II1 - 2771 - 277
41GLYGLYPROPROchain 'M' and (resseq 1:277 )MM1 - 2771 - 277
12ARGARGARGARGchain 'D' and (resseq 5:190 )DD5 - 1906 - 191
22ARGARGARGARGchain 'H' and (resseq 5:190 )HH5 - 1906 - 191
32ARGARGARGARGchain 'L' and (resseq 5:190 )LL5 - 1906 - 191
42ARGARGARGARGchain 'P' and (resseq 5:190 )PP5 - 1906 - 191
13METMETMETMETchain 'B' and (resseq 0:99 )BB0 - 991 - 100
23METMETMETMETchain 'F' and (resseq 0:99 )FF0 - 991 - 100
33METMETMETMETchain 'J' and (resseq 0:99 )JJ0 - 991 - 100
43METMETMETMETchain 'N' and (resseq 0:99 )NN0 - 991 - 100
14SERSERLEULEUchain 'C' and (resseq 1:8 )CC1 - 81 - 8
24SERSERLEULEUchain 'G' and (resseq 1:8 )GG1 - 81 - 8
34SERSERLEULEUchain 'K' and (resseq 1:8 )KK1 - 81 - 8
44SERSERLEULEUchain 'O' and (resseq 1:8 )OO1 - 81 - 8

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(-0.999943, -0.010689, -0.000431), (0.010654, -0.998721, 0.04942), (-0.000959, 0.049413, 0.998778)-1.98889, 6.00673, -0.261628
2given(-0.402409, -0.915458, -0.001919), (-0.914311, 0.402008, -0.049237), (0.045846, -0.018059, -0.998785)-36.596901, -9.47167, -56.515999
3given(0.398668, 0.91701, 0.012516), (0.917093, -0.398661, -0.003213), (0.002043, 0.012759, -0.999917)34.633598, 12.8478, -56.3442
4given(-0.999977, -0.006619, -0.001104), (0.006564, -0.998994, 0.044359), (-0.001396, 0.044351, 0.999015)-1.89813, 5.65823, -0.273655
5given(-0.399154, -0.916882, -0.001687), (-0.916071, 0.398877, -0.041366), (0.038601, -0.014966, -0.999143)-36.512501, -9.76068, -56.596001
6given(0.398647, 0.917095, 0.004267), (0.917088, -0.398607, -0.007873), (-0.005519, 0.007052, -0.99996)34.635201, 12.9628, -56.530499
7given(-0.999898, -0.011552, -0.008399), (0.01122, -0.999195, 0.038506), (-0.008837, 0.038408, 0.999223)-2.40128, 5.38897, -0.493067
8given(-0.403126, -0.915138, 0.00347), (-0.914245, 0.402559, -0.045843), (0.040556, -0.021653, -0.998943)-36.584099, -9.45763, -56.889599
9given(0.394744, 0.918733, 0.010334), (0.918789, -0.394694, -0.006582), (-0.001968, 0.012093, -0.999925)34.598598, 12.8839, -56.445202
10given(-0.999933, -0.010359, -0.00508), (0.010099, -0.998758, 0.048796), (-0.005579, 0.048742, 0.998796)-2.3336, 5.96404, -0.346973
11given(-0.417026, -0.908866, -0.007223), (-0.907765, 0.41689, -0.046529), (0.0453, -0.012846, -0.998891)-36.596901, -8.45064, -56.154099
12given(0.382956, 0.923717, 0.009563), (0.923725, -0.383016, 0.005493), (0.008737, 0.00673, -0.999939)34.037201, 13.1624, -56.1264

-
Components

#1: Protein
H-2 class I histocompatibility antigen, K-B alpha chain / MHC class I H-2KB heavy chain / H-2K(B)


Mass: 32256.959 Da / Num. of mol.: 4 / Fragment: extracellular domain (UNP residues 22-301)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H-2KB, H2-K, H2-K1 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P01901
#2: Protein
Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 4 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, BETA-2 MICROGLOBULIN, CDABP0092, HDCMA22P / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P61769
#3: Protein/peptide
Ovalbumin / / Allergen Gal d II / Egg albumin / Plakalbumin


Mass: 964.137 Da / Num. of mol.: 4 / Fragment: UNP residues 258-265 / Source method: obtained synthetically / Source: (synth.) Gallus gallus (chicken) / References: UniProt: P01012
#4: Protein
CPXV203 protein


Mass: 23896.361 Da / Num. of mol.: 4 / Fragment: UNP residues 17-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cowpox virus / Strain: Brighton Red / Gene: CPXV203, CPXV203 CDS / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q8QMP2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.55
Details: 10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97909 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Sep 10, 2010
RadiationMonochromator: Rosenbaum-Rock monochromator 1: high-resolution double crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97909 Å / Relative weight: 1
ReflectionRedundancy: 4.1 % / Av σ(I) over netI: 7.25 / Number: 198533 / Rmerge(I) obs: 0.164 / Χ2: 1.04 / D res high: 3 Å / D res low: 50 Å / Num. obs: 47950 / % possible obs: 87.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.455099.710.1071.0384.3
4.335.4592.410.1351.054
3.784.3383.610.1870.9974.1
3.433.7883.110.2771.0084.1
3.193.4383.810.3691.0644.2
33.1984.910.6221.064.2
ReflectionResolution: 3→50 Å / Num. all: 47950 / Num. obs: 47882 / % possible obs: 87.9 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 70.46 Å2 / Rmerge(I) obs: 0.164 / Χ2: 1.036 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
3-3.194.20.6222.5577141.0684.9
3.19-3.434.20.369476291.06483.8
3.43-3.784.10.2774.1975481.00883.1
3.78-4.334.10.1875.9375840.99783.6
4.33-5.4540.1358.4784011.0592.4
5.45-504.30.10710.890741.03899.7

-
Phasing

Phasing
Method
SAD
molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.95 Å71.74 Å
Translation2.95 Å71.74 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
SOLVEphasing
RESOLVEphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
Blu-IceICEdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CLZ

2clz


Resolution: 3→49.36 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.47 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.96 / σ(I): 1.96 / Phase error: 28.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2394 5 %RANDOM
Rwork0.2295 ---
obs0.2307 47882 87.16 %-
all-47950 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.295 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 243.52 Å2 / Biso mean: 83.3211 Å2 / Biso min: 14.43 Å2
Baniso -1Baniso -2Baniso -3
1--3.3931 Å21.0886 Å24.4702 Å2
2---3.7601 Å24.2764 Å2
3---7.1532 Å2
Refinement stepCycle: LAST / Resolution: 3→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18588 0 0 72 18660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00219096
X-RAY DIFFRACTIONf_angle_d0.53825840
X-RAY DIFFRACTIONf_chiral_restr0.0412720
X-RAY DIFFRACTIONf_plane_restr0.0023360
X-RAY DIFFRACTIONf_dihedral_angle_d9.6627060
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2255X-RAY DIFFRACTIONPOSITIONAL0.003
12E2255X-RAY DIFFRACTIONPOSITIONAL0.003
13I2255X-RAY DIFFRACTIONPOSITIONAL0.003
14M2255X-RAY DIFFRACTIONPOSITIONAL0.003
21D1489X-RAY DIFFRACTIONPOSITIONAL0.003
22H1489X-RAY DIFFRACTIONPOSITIONAL0.003
23L1489X-RAY DIFFRACTIONPOSITIONAL0.003
24P1489X-RAY DIFFRACTIONPOSITIONAL0.003
31B837X-RAY DIFFRACTIONPOSITIONAL0.003
32F837X-RAY DIFFRACTIONPOSITIONAL0.003
33J837X-RAY DIFFRACTIONPOSITIONAL0.003
34N837X-RAY DIFFRACTIONPOSITIONAL0.003
41C68X-RAY DIFFRACTIONPOSITIONAL0.003
42G68X-RAY DIFFRACTIONPOSITIONAL0.003
43K68X-RAY DIFFRACTIONPOSITIONAL0.003
44O68X-RAY DIFFRACTIONPOSITIONAL0.003
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
3-3.06130.38871220.350622442366224473
3.0613-3.12790.32551390.319826132752261385
3.1279-3.20060.37031380.289526312769263185
3.2006-3.28060.32071360.281726072743260784
3.2806-3.36930.28841340.268125312665253184
3.3693-3.46850.34781330.287725522685255283
3.4685-3.58040.281360.272525682704256883
3.5804-3.70830.27981340.296325402674254083
3.7083-3.85670.29011310.249725262657252683
3.8567-4.03220.27611340.257325182652251882
4.0322-4.24460.25061370.213925862723258684
4.2446-4.51040.21891350.198226382773263886
4.5104-4.85840.19281490.1928102959281091
4.8584-5.34680.22361540.194429553109295597
5.3468-6.11920.24171610.209530493210304999
6.1192-7.70490.25191610.2111305432153054100
7.7049-49.36690.20511600.1968306632263066100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.45820.1157-2.70522.87150.20665.8875-0.0495-0.9183-0.42540.4820.2432-0.21410.31730.7403-0.23430.46180.1025-0.17020.47780.01010.55421.5182-9.6231-48.3829
23.266-2.36750.13045.9635-0.50725.6540.1237-0.53730.91780.4171-0.1003-0.3021-0.83160.0578-0.03520.5952-0.0863-0.02590.661-0.37410.90878.167625.7786-46.2656
30.97610.66481.46914.36130.85282.9767-0.1301-0.8051.2640.40910.0634-0.6904-0.59770.55570.05120.5607-0.1927-0.05110.904-0.48011.211929.72217.6421-47.6419
42.0105-4.90782.00842.05482.30832.0106-0.3523-1.6548-1.2499-0.1110.41090.30241.55171.87830.02110.59010.17070.10740.6306-0.02670.930823.5674-16.3791-50.0576
54.55580.373-0.56964.0369-0.48123.40770.14740.29630.4628-0.3307-0.0278-0.1865-0.12930.1525-0.10510.3502-0.00390.05210.50020.00540.456415.657311.1008-72.32
64.9244-0.26011.66742.280.18626.3603-0.021-0.84330.20080.31870.2010.1308-0.3848-0.4483-0.19480.49260.02050.07990.41530.00760.3554-23.62612.9808-48.845
74.9044-2.30240.39858.87040.69476.35320.461-0.0907-0.90130.3298-0.262-0.15730.75180.5031-0.19580.43940.0743-0.02110.67210.23410.8014-9.9012-22.1283-44.975
81.74121.2408-1.25565.2681-0.33762.94640.0574-0.6994-0.88230.4519-0.09821.00790.636-0.41620.06520.4902-0.0773-0.01680.6790.26681.05-31.5659-14.4252-46.9102
99.4934-2.23012.00512.01991.01991.99350.4843-0.39350.75190.26130.8828-1.2726-2.8198-0.586-1.06431.1978-0.14790.02080.6044-0.00770.5414-25.847619.6241-50.8726
103.922-0.08360.42944.1004-1.19964.19920.03650.4408-0.724-0.43250.06030.10480.19550.0985-0.05930.3994-0.0074-0.10920.4821-0.15750.5754-17.4188-8.7487-71.7534
112.68880.32090.08425.1767-1.76175.2074-0.18580.3905-0.1683-1.14920.5078-0.28610.606-0.089-0.31530.6286-0.0933-0.06260.5397-0.17170.5289-22.8747-53.4096-8.2273
127.1544-3.5765-1.01465.46340.41457.28150.17260.38860.175-0.38040.17480.6929-0.7116-0.3296-0.39350.8863-0.1852-0.26560.5350.17480.8328-49.7733-26.9944-12.0593
135.0565-0.7350.5441.22070.36083.0259-0.17960.6535-0.3264-0.7550.11631.274-0.0272-0.41660.02910.7993-0.259-0.45490.70840.21121.1453-51.1305-49.9702-10.2502
142.0354.6469-8.9941.98581.99331.99940.21550.60520.6462-0.70670.4288-0.95711.86891.5351-0.51930.684-0.0103-0.09810.8806-0.04810.5366-17.6167-58.065-6.1555
154.25840.2548-0.37775.0695-0.69414.44760.0964-0.27220.18630.25660.08130.5662-0.1359-0.0986-0.20070.4091-0.07810.02860.40640.07760.4902-40.5414-39.277114.7596
162.66720.44531.28065.48522.62095.1293-0.01650.26040.236-1.08780.3236-0.0591-0.7059-0.0994-0.31520.56480.01790.10530.43990.11210.519-25.8203-2.9672-8.0526
174.2494-3.2573-0.04616.3217-0.46074.0912-0.25650.1811-0.5109-0.44620.3927-1.12790.49920.5093-0.07370.93330.01030.37890.5537-0.28371.2351.3282-29.2959-10.4506
183.4992-1.0124-0.3981.6371-0.37482.6921-0.070.52160.0722-0.76730.0913-1.8629-0.11940.6979-0.12860.7766-0.20560.55480.7167-0.35371.6562.4295-6.2519-8.8844
198.31710.44172.21852.03521.9922.00220.45430.1283-0.2679-0.601-0.7840.4527-2.5267-1.3520.20110.74140.00060.11110.5474-0.04930.4431-31.24471.6846-6.3309
203.0393-0.0221-0.31664.1610.40653.850.0488-0.1388-0.26810.30820.1313-0.72670.10360.1201-0.17520.4795-0.0487-0.10580.4873-0.1840.7525-9.1859-16.773615.7226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:180)A1 - 180
2X-RAY DIFFRACTION2chain 'A' and (resseq 181:277)A181 - 277
3X-RAY DIFFRACTION3chain 'B' and (resseq 0:99)B0 - 99
4X-RAY DIFFRACTION4chain 'C' and (resseq 1:8)C1 - 8
5X-RAY DIFFRACTION5chain 'D' and (resseq 5:190)D5 - 190
6X-RAY DIFFRACTION6chain 'E' and (resseq 1:180)E1 - 180
7X-RAY DIFFRACTION7chain 'E' and (resseq 181:277)E181 - 277
8X-RAY DIFFRACTION8chain 'F' and (resseq 0:99)F0 - 99
9X-RAY DIFFRACTION9chain 'G' and (resseq 1:8)G1 - 8
10X-RAY DIFFRACTION10chain 'H' and (resseq 5:190)H5 - 190
11X-RAY DIFFRACTION11chain 'I' and (resseq 1:180)I1 - 180
12X-RAY DIFFRACTION12chain 'I' and (resseq 181:277)I181 - 277
13X-RAY DIFFRACTION13chain 'J' and (resseq 0:99)J0 - 99
14X-RAY DIFFRACTION14chain 'K' and (resseq 1:8)K1 - 8
15X-RAY DIFFRACTION15chain 'L' and (resseq 5:190)L5 - 190
16X-RAY DIFFRACTION16chain 'M' and (resseq 1:180)M1 - 180
17X-RAY DIFFRACTION17chain 'M' and (resseq 181:277)M181 - 277
18X-RAY DIFFRACTION18chain 'N' and (resseq 0:99)N0 - 99
19X-RAY DIFFRACTION19chain 'O' and (resseq 1:8)O1 - 8
20X-RAY DIFFRACTION20chain 'P' and (resseq 5:190)P5 - 190

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more