[English] 日本語
Yorodumi
- PDB-4y2d: Crystal structure of the mCD1d/7DW8-5/iNKTCR ternary complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y2d
TitleCrystal structure of the mCD1d/7DW8-5/iNKTCR ternary complex
Components
  • (Chimeric TCR ...) x 2
  • Antigen-presenting glycoprotein CD1d1
  • Beta-2-microglobulinBeta-2 microglobulin
KeywordsIMMUNE SYSTEM / MHC-fold / Ig-fold / glycolipid antigen presentation / T cell receptor
Function / homology
Function and homology information


regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / lipid antigen binding / positive regulation of NK T cell activation / NK T cell differentiation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / lipid antigen binding / positive regulation of NK T cell activation / NK T cell differentiation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive thymic T cell selection / positive regulation of macrophage activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of membrane depolarization / antigen processing and presentation / positive regulation of interleukin-4 production / regulation of immune response / cellular defense response / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / Neutrophil degranulation / cell adhesion molecule binding / T cell receptor binding / response to bacterium / 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 / 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 / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / positive regulation of type II interferon production / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / negative regulation of neuron projection development / late endosome / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / histone binding / protein refolding / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / lysosome / learning or memory / early endosome / endosome membrane / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
MHC-I family domain / Domain of unknown function (DUF1968) / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Immunoglobulin V-Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein ...MHC-I family domain / Domain of unknown function (DUF1968) / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Immunoglobulin V-Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
Chem-7DW / alpha-L-fucopyranose / T cell receptor alpha variable 11 / Beta-chain / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsZajonc, D.M. / Yu, E.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI074952 United States
CitationJournal: To Be Published
Title: Structural modifications of alphaGalCer in both lipid and carbohydrate moiety influence activation of murine and human iNKT cells
Authors: Birkholz, A. / Nemcovic, M. / Yu, E.D. / Girardi, E. / Wang, J. / Khurana, A. / Pauwels, N. / Franck, R.W. / Tsuji, M. / Howell, A. / Calenbergh, S. / Kronenberg, M. / Zajonc, D.M.
History
DepositionFeb 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Nov 29, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id
Revision 2.1Dec 11, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Sep 27, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antigen-presenting glycoprotein CD1d1
B: Beta-2-microglobulin
C: Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)
D: Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)
E: Antigen-presenting glycoprotein CD1d1
F: Beta-2-microglobulin
G: Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)
H: Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,93017
Polymers188,7518
Non-polymers3,1799
Water0
1
A: Antigen-presenting glycoprotein CD1d1
B: Beta-2-microglobulin
C: Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)
D: Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,7818
Polymers94,3764
Non-polymers1,4064
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Antigen-presenting glycoprotein CD1d1
F: Beta-2-microglobulin
G: Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)
H: Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1499
Polymers94,3764
Non-polymers1,7735
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.422, 150.264, 100.800
Angle α, β, γ (deg.)90.000, 96.240, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12B
22F
13C
23G
14D
24H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 280
2114E1 - 280
1124B1 - 100
2124F1 - 100
1134C1 - 210
2134G1 - 210
1144D1 - 250
2144H1 - 250

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.997578, -0.033907, 0.060737), (0.033131, -0.999357, -0.013742), (0.061164, -0.011697, 0.998059)24.86112, -37.81958, -0.19629
3given(1), (1), (1)
4given(-0.996659, -0.04813, 0.065985), (0.047908, -0.998839, -0.004938), (0.066146, -0.001761, 0.997808)24.14159, -38.582081, 0.00479
5given(1), (1), (1)
6given(-0.999713, -0.00016, 0.02395), (0.000169, -1, 0.000354), (0.02395, 0.000358, 0.999713)27.228661, -38.245419, 0.55387
7given(1), (1), (1)
8given(-0.999918, -0.001527, 0.012746), (0.001457, -0.999984, -0.005499), (0.012754, -0.00548, 0.999904)27.98807, -37.80426, 0.12503

-
Components

-
Protein , 2 types, 4 molecules AEBF

#1: Protein Antigen-presenting glycoprotein CD1d1


Mass: 32632.668 Da / Num. of mol.: 2 / Fragment: Ectodomain, UNP residues 19-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, Cd1.1 / Plasmid: pBACpHp10 / Details (production host): dual promotor / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P11609
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11660.350 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pBACp10pH / Details (production host): dual promotor / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P01887

-
Chimeric TCR ... , 2 types, 4 molecules CGDH

#3: Protein Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain) / Protein Trav11d / Human nkt tcr beta chain


Mass: 23055.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Gene: Trav11, Trav11d, HDCMA22P / Plasmid: pET22b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: A0A0B4J1J9*PLUS
#4: Protein Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain) / Beta-chain / T-cell receptor beta-2 chain C region


Mass: 27026.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Gene: TRBC2, TCRBC2 / Plasmid: pET22b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: A2NTY6*PLUS

-
Sugars , 3 types, 7 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: 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.: 5 / Source method: obtained synthetically / 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
#8: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 1 types, 2 molecules

#7: Chemical ChemComp-7DW / 11-(4-fluorophenyl)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]undecanamide


Mass: 742.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H72FNO9

-
Details

Sequence detailsChimeric TCR Valpha14Jalpha18 chain (chain C) is made of: Mouse variable domain ...Chimeric TCR Valpha14Jalpha18 chain (chain C) is made of: Mouse variable domain (MKTQVEQSPQSLVVRQGENCVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSNGRYSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGRLHFGAGTQLIVI) and Human constant domain (PDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS) Chimeric TCR Vbeta8.2 chain (chain D) is made of: Mouse variable domain (MEAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGDEGYTQYFGPGTRLLVLEDLRNVTPPKVSLFEPSK) and Human constant domain (AEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.45 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop / Details: 17% PEG 4000, 8% tascimate pH 4.0 / PH range: 4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2011
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 44418 / % possible obs: 99.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.093 / Χ2: 1.373 / Net I/av σ(I): 13.194 / Net I/σ(I): 7.9 / Num. measured all: 135018
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.05-3.1230.53629501.02999.8
3.12-3.230.43329751.04499.8
3.2-3.2930.3429331.11799.5
3.29-3.3830.2629641.18999.8
3.38-3.4930.20729651.23399.8
3.49-3.6230.17929931.25599.9
3.62-3.7630.14929711.36299.8
3.76-3.9330.12629441.47999.9
3.93-4.1430.10529721.62799.7
4.14-4.430.08629901.81699.7
4.4-4.743.10.07129501.82399.5
4.74-5.213.10.06529641.62299.2
5.21-5.9730.06729551.46398.9
5.97-7.513.10.05729661.37698.2
7.51-503.10.03129261.14396.1

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q7Y and 3QUZ

2q7y

3quz


Resolution: 3.05→49.41 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.883 / SU B: 45.123 / SU ML: 0.363 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 1388 3.1 %RANDOM
Rwork0.2168 43007 --
obs0.2181 43007 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 182.39 Å2 / Biso mean: 70.5 Å2 / Biso min: 39.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-0.19 Å2
2---0.06 Å20 Å2
3---0.21 Å2
Refinement stepCycle: final / Resolution: 3.05→49.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11627 0 316 0 11943
Biso mean--74.1 --
Num. residues----1559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0212272
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210655
X-RAY DIFFRACTIONr_angle_refined_deg0.9941.9516783
X-RAY DIFFRACTIONr_angle_other_deg0.8033.01324344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.59751541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4524.217517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.081151591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3831550
X-RAY DIFFRACTIONr_chiral_restr0.0560.21890
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02114086
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022890
X-RAY DIFFRACTIONr_mcbond_it0.4682.416218
X-RAY DIFFRACTIONr_mcbond_other0.4682.416217
X-RAY DIFFRACTIONr_mcangle_it0.8393.6157741
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3232MEDIUM POSITIONAL0.250.5
1A3232MEDIUM THERMAL1.942
2B1041MEDIUM POSITIONAL0.290.5
2B1041MEDIUM THERMAL2.582
3C2815MEDIUM POSITIONAL0.20.5
3C2815MEDIUM THERMAL1.212
4D3434MEDIUM POSITIONAL0.230.5
4D3434MEDIUM THERMAL1.132
LS refinement shellResolution: 3.051→3.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 104 -
Rwork0.315 3126 -
all-3230 -
obs--99.26 %
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)
13.81351.20980.90963.37620.28611.7833-0.05380.5185-0.4639-0.30350.0245-0.08090.1327-0.14940.02930.3370.0555-0.03220.4081-0.12220.379919.5720.47722.841
20.5868-0.5114-0.99465.7588-1.13422.61380.11870.77660.2315-1.06350.41640.0905-0.1393-1.427-0.53510.7864-0.0974-0.23232.3363-0.01210.3684-9.5061.9743.674
310.97992.7683-0.28552.3380.11882.2134-0.27360.7375-0.1499-0.00890.24130.31780.3126-0.6160.03240.40250.0149-0.10270.7924-0.16170.4239-8.857-1.24723.03
45.8103-1.91852.17572.3375-0.75181.9373-0.06360.17-0.12310.1522-0.0176-0.05340.0320.07360.08120.2432-0.006-0.0630.2332-0.06190.309747.721-7.8441.903
52.2673-0.95321.55833.4061-0.6817.107-0.1121-0.57140.20370.44780.11620.0141-0.4252-0.1172-0.00410.3669-0.0079-0.01490.3727-0.13070.342535.3116.37755.951
64.0748-0.152-1.88465.56081.95085.0133-0.0273-0.1803-0.37560.92130.0864-0.24321.11050.5142-0.05910.7270.0521-0.30690.4884-0.05860.685970.427-10.01769.569
76.617-0.5256-0.65823.50421.03263.98440.0364-0.3594-0.56510.5995-0.0893-0.01540.2946-0.06830.05280.5264-0.0488-0.16580.3228-0.03790.30160.5464.00472.257
82.7454-0.0542-1.54034.78280.38382.65060.13590.04710.0747-0.99960.1645-0.5595-0.30870.2784-0.30040.5119-0.03450.17830.3302-0.07350.3767.87-38.42922.034
95.25890.8166-2.04822.4682.5425.40220.27960.44080.2851-0.47780.3783-0.5669-0.19090.553-0.65791.0172-0.21440.76691.0546-0.22991.064834.294-37.9431.099
104.27590.44241.89060.25020.29992.77710.022-0.3874-0.1906-0.23490.1885-0.6195-0.37431.0247-0.21050.5939-0.23810.72910.9773-0.48641.796234.689-36.57120.958
115.4767-2.6059-2.8973.9171.26222.682-0.00740.1308-0.1083-0.0968-0.06070.388-0.0652-0.01680.06810.2061-0.0035-0.07470.20530.02470.2674-19.466-30.47741.967
121.695-0.4686-1.10162.45840.29087.0196-0.1788-0.401-0.23470.5845-0.0635-0.08730.58440.30970.24220.35370.0104-0.01470.3850.11030.3194-6.704-44.43255.591
134.9661-1.64821.04424.6381-2.46856.6938-0.0623-0.11750.71971.12470.16030.5085-1.4101-0.63-0.0980.76190.02870.34970.4135-0.00460.8282-41.59-28.39470.181
145.9750.1461.11773.9601-1.02713.96540.1542-0.32990.37170.6185-0.1880.1578-0.3469-0.0310.03380.4971-0.07230.12490.29950.02810.2212-31.969-42.36671.964
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 185
2X-RAY DIFFRACTION1A302 - 303
3X-RAY DIFFRACTION1E505
4X-RAY DIFFRACTION1A304
5X-RAY DIFFRACTION2A186 - 275
6X-RAY DIFFRACTION3B1 - 97
7X-RAY DIFFRACTION4C2 - 114
8X-RAY DIFFRACTION5D2 - 112
9X-RAY DIFFRACTION6C115 - 204
10X-RAY DIFFRACTION7D113 - 240
11X-RAY DIFFRACTION8E6 - 185
12X-RAY DIFFRACTION8A301
13X-RAY DIFFRACTION8E501 - 504
14X-RAY DIFFRACTION8E506
15X-RAY DIFFRACTION9E186 - 275
16X-RAY DIFFRACTION10F2 - 97
17X-RAY DIFFRACTION11G2 - 114
18X-RAY DIFFRACTION12H2 - 112
19X-RAY DIFFRACTION13G115 - 204
20X-RAY DIFFRACTION14H113 - 240

+
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