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- PDB-4ei5: Crystal Structure of XV19 TCR in complex with CD1d-sulfatide C24:1 -

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Basic information

Entry
Database: PDB / ID: 4ei5
TitleCrystal Structure of XV19 TCR in complex with CD1d-sulfatide C24:1
Components
  • Antigen-presenting glycoprotein CD1d1
  • Beta-2-microglobulin
  • Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
  • Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
KeywordsIMMUNE SYSTEM / sulfatide / lipid / CD1d / NKT typeII / TCR
Function / homology
Function and homology information


regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / 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 regulation of macrophage activation ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / 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 regulation of macrophage activation / positive thymic T cell selection / 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 / positive regulation of interleukin-4 production / antigen processing and presentation / regulation of immune response / cellular defense response / T cell receptor binding / positive regulation of interleukin-2 production / Neutrophil degranulation / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / late endosome / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / early endosome / learning or memory / lysosome / endosome membrane / immune response / external side of plasma membrane / lysosomal membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 ...MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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
Chem-CIS / CITRATE ANION / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsPatel, O. / Gras, S. / Rossjohn, J.
CitationJournal: Nat.Immunol. / Year: 2012
Title: Recognition of CD1d-sulfatide mediated by a type II natural killer T cell antigen receptor.
Authors: Patel, O. / Pellicci, D.G. / Gras, S. / Sandoval-Romero, M.L. / Uldrich, A.P. / Mallevaey, T. / Clarke, A.J. / Le Nours, J. / Theodossis, A. / Cardell, S.L. / Gapin, L. / Godfrey, D.I. / Rossjohn, J.
History
DepositionApr 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Sep 5, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_ref_seq_dif / 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_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.id / _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_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_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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_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.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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 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: Antigen-presenting glycoprotein CD1d1
B: Beta-2-microglobulin
C: Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
D: Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
E: Antigen-presenting glycoprotein CD1d1
F: Beta-2-microglobulin
G: Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
H: Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,82117
Polymers195,2258
Non-polymers4,5969
Water00
1
A: Antigen-presenting glycoprotein CD1d1
B: Beta-2-microglobulin
C: Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
D: Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0869
Polymers97,6124
Non-polymers2,4745
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Antigen-presenting glycoprotein CD1d1
F: Beta-2-microglobulin
G: Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
H: Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7358
Polymers97,6124
Non-polymers2,1224
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.739, 140.711, 160.773
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Antigen-presenting glycoprotein CD1d1 / CD1d


Mass: 34662.012 Da / Num. of mol.: 2 / Fragment: UNP residues 19-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, Cd1.1 / Plasmid: pFasBacpHp10 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P11609
#2: Protein 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: pFasBacpHp10 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01887
#3: Protein Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)


Mass: 23209.518 Da / Num. of mol.: 2 / Fragment: extracellular domain (SEE REMARK 999)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#4: Protein Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)


Mass: 28080.617 Da / Num. of mol.: 2 / Fragment: extracellular domain (SEE REMARK 999)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Sugars , 4 types, 6 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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.: 2
Source method: isolated from a genetically manipulated source
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
#7: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#8: 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.: 2
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

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Non-polymers , 2 types, 3 molecules

#9: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#10: Chemical ChemComp-CIS / (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE / (2S,3R,4E)-N-NERVONIC-1-[BETA-D-(3-SULFATE)-GALACTOPYRANOSYL]-2-AMINO-OCTADECENE-3-OL / CIS-TETRACOSENOYL SULFATIDE


Mass: 890.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C48H91NO11S

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Details

Sequence detailsTHE AUTHORS STATE THAT D201H IN CHAINS A AND E IS CORRECT AS PER BRADBURY ET AL, 1988 (PMID 2460336) ...THE AUTHORS STATE THAT D201H IN CHAINS A AND E IS CORRECT AS PER BRADBURY ET AL, 1988 (PMID 2460336). IN CHAINS B AND F, D85A IS A NATURAL VARIANT. CHAINS C AND G ARE CHIMERAS COMPRISING THE MOUSE VARIABLE DOMAIN (RESIDUES 1-116) AND HUMAN CONSTANT DOMAIN (RESIDUES 117-207). CHAINS D AND H ARE CHIMERAS COMPRISING THE MOUSE VARIABLE DOMAIN (RESIDUES 1-114) AND HUMAN CONSTANT DOMAIN (RESIDUES 115-244).

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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: 2.95 Å3/Da / Density % sol: 58.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 25% PEG3350, 0.1 M citrate/Bis-Tris-propane, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95453 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95453 Å / Relative weight: 1
ReflectionResolution: 3.1→140 Å / Num. all: 42432 / Num. obs: 42432 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 90.04 Å2 / Rmerge(I) obs: 0.151 / Net I/σ(I): 8.3
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.107 / Mean I/σ(I) obs: 1.5 / Num. unique all: 6151 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.12data scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2AKR AND 4EI6

2akr

4ei6


Resolution: 3.1→105.88 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 0.48 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.383 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 2152 5.08 %RANDOM
Rwork0.1972 ---
obs0.1988 42390 98.56 %-
Displacement parametersBiso max: 222.1 Å2 / Biso mean: 100.8742 Å2 / Biso min: 31.75 Å2
Baniso -1Baniso -2Baniso -3
1--6.6184 Å20 Å20 Å2
2--19.9022 Å20 Å2
3----13.2839 Å2
Refine analyzeLuzzati coordinate error obs: 0.666 Å
Refinement stepCycle: LAST / Resolution: 3.1→105.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12928 0 275 0 13203
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4516SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes347HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1937HARMONIC5
X-RAY DIFFRACTIONt_it13610HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1744SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14200SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13610HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg18515HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion2.29
X-RAY DIFFRACTIONt_other_torsion20.6
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2945 182 5.82 %
Rwork0.2492 2946 -
all0.2519 3128 -
obs--98.56 %
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)
11.2578-0.33-0.05033.10992.50053.0213-0.0097-0.17750.0182-0.00330.2282-0.12660.15320.3527-0.2185-0.32210.00050.1324-0.11050.0033-0.024342.4762-31.71636.5051
23.3575-1.2257-1.06583.59433.21252.5981-0.1119-0.3658-0.03820.1262-0.09690.10070.1175-0.07040.2088-0.1992-0.0340.14710.0026-0.0430.005231.1088-24.982717.7092
30.74530.2444-0.04073.96722.06271.8543-0.03690.5378-0.2298-0.54140.2368-0.3477-0.2787-0.0941-0.1999-0.275-0.03560.0460.1628-0.25790.004347.9568-70.2849-39.4515
42.0845-0.27490.335.11162.41451.98410.18340.33320.0478-1.0885-0.06730.1675-0.3504-0.4275-0.1161-0.1799-0.0675-0.14450.00460.0129-0.274528.364-67.2973-41.3584
51.69220.80740.09915.88992.92582.1904-0.22050.1756-0.2419-0.97150.1227-0.1466-0.36160.07940.09780.0552-0.11680.0261-0.32610.095-0.010317.7688-36.2791-71.8249
63.3871.66931.11720.04430.2643.8603-0.01510.2583-0.0215-0.326-0.27070.2582-0.1961-0.50240.28580.152-0.0092-0.2393-0.3253-0.05670.16193.3169-45.6554-79.0545
71.73781.931-0.01844.74170.49913.88020.247-0.4629-0.20230.5251-0.3017-0.1526-0.36670.26590.0548-0.2625-0.0302-0.0469-0.03860.1941-0.10435.02886.2914-41.9677
81.18750.1165-0.2453.19431.09773.16610.1026-0.52630.06060.7308-0.08440.6021-0.5335-0.5198-0.0181-0.00460.05230.2834-0.08550.0435-0.128816.66555.3341-30.575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A7 - 1
2X-RAY DIFFRACTION2{ B|* }B2 - 99
3X-RAY DIFFRACTION3{ C|* }C2 - 202
4X-RAY DIFFRACTION4{ D|* }D2 - 243
5X-RAY DIFFRACTION5{ E|* }E7 - 311
6X-RAY DIFFRACTION6{ F|* }F2 - 96
7X-RAY DIFFRACTION7{ G|* }G2 - 202
8X-RAY DIFFRACTION8{ H|* }H1 - 237

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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

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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

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