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- PDB-1w72: Crystal structure of HLA-A1:MAGE-A1 in complex with Fab-Hyb3 -

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Basic information

Entry
Database: PDB / ID: 1w72
TitleCrystal structure of HLA-A1:MAGE-A1 in complex with Fab-Hyb3
Components
  • BETA-2-MICROGLOBULIN
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN
  • HYB3 HEAVY CHAIN
  • HYB3 LIGHT CHAIN
  • MELANOMA-ASSOCIATED ANTIGEN 1
KeywordsIMMUNE SYSTEM / HLA/FAB FRAGMENT / HUMAN LEUCOCYTE ANTIGEN / PEPTIDE-SPECIFIC FAB / TCR-LIKE BINDING / MHC-I
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / CD8 receptor binding ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / CD8 receptor binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / negative regulation of Notch signaling pathway / detection of bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / positive regulation of type II interferon production / recycling endosome membrane / histone deacetylase binding / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / T cell receptor signaling pathway / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / ER-Phagosome pathway / protein refolding / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / external side of plasma membrane / innate immune response / lysosomal membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / Golgi apparatus
Similarity search - Function
Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen ...Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Melanoma-associated antigen 1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHulsmeyer, M. / Chames, P. / Hillig, R.C. / Stanfield, R.L. / Held, G. / Coulie, P.G. / Alings, C. / Wille, G. / Saenger, W. / Uchanska-Ziegler, B. ...Hulsmeyer, M. / Chames, P. / Hillig, R.C. / Stanfield, R.L. / Held, G. / Coulie, P.G. / Alings, C. / Wille, G. / Saenger, W. / Uchanska-Ziegler, B. / Hoogenboom, H.R. / Ziegler, A.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: A Major Histocompatibility Complex.Peptide- Restricted Antibody and T Cell Receptor Molecules Recognize Their Target by Distinct Binding Modes: Crystal Structure of Human Leukocyte Antigen ...Title: A Major Histocompatibility Complex.Peptide- Restricted Antibody and T Cell Receptor Molecules Recognize Their Target by Distinct Binding Modes: Crystal Structure of Human Leukocyte Antigen (Hla)-A1.Mage-A1 in Complex with Fab-Hyb3
Authors: Hulsmeyer, M. / Chames, P. / Hillig, R.C. / Stanfield, R.L. / Held, G. / Coulie, P.G. / Alings, C. / Wille, G. / Saenger, W. / Uchanska-Ziegler, B. / Hoogenboom, H.R. / Ziegler, A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Direct Selection of a Human Antibody Fragment Directed Against the Tumor T-Cell Epitope Hla-A1- Mage-A1 from a Nonimmunized Phage-Fab Library
Authors: Chames, P. / Hufton, S.E. / Coulie, P.G. / Uchanska-Ziegler, B. / Hoogenboom, H.R.
#2: Journal: J.Immunol. / Year: 2002
Title: Tcr-Like Human Antibodies Expressed on Human Ctls Mediate Antibody Affinity-Dependent Cytolytic Activity
Authors: Chames, P. / Willemsen, R.A. / Rojas, G. / Dieckmann, D. / Rem, L. / Schuler, G. / Bolhuis, R.L. / Hoogenboom, H.R.
History
DepositionAug 27, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN
B: BETA-2-MICROGLOBULIN
C: MELANOMA-ASSOCIATED ANTIGEN 1
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN
E: BETA-2-MICROGLOBULIN
F: MELANOMA-ASSOCIATED ANTIGEN 1
H: HYB3 HEAVY CHAIN
I: HYB3 HEAVY CHAIN
L: HYB3 LIGHT CHAIN
M: HYB3 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,09414
Polymers181,72610
Non-polymers3684
Water11,764653
1
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN
B: BETA-2-MICROGLOBULIN
C: MELANOMA-ASSOCIATED ANTIGEN 1
H: HYB3 HEAVY CHAIN
L: HYB3 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0477
Polymers90,8635
Non-polymers1842
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10760 Å2
ΔGint-51.4 kcal/mol
Surface area43900 Å2
MethodPISA
2
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN
E: BETA-2-MICROGLOBULIN
F: MELANOMA-ASSOCIATED ANTIGEN 1
I: HYB3 HEAVY CHAIN
M: HYB3 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0477
Polymers90,8635
Non-polymers1842
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
ΔGint-57.9 kcal/mol
Surface area44100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.359, 50.050, 136.705
Angle α, β, γ (deg.)90.00, 109.85, 90.00
Int Tables number4
Space group name H-MP1211
DetailsSUBUNIT: DIMER OF ALPHA CHAIN AND A BETA CHAIN(BETA-2-MICROGLOBULIN).

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN / HUMAN LYMPHOCYTE ANTIGEN HLA-A1 / A-1 ALPHA CHAIN PRECURSOR MHC CLASS I ANTIGEN A*1


Mass: 31636.955 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 25-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P30443, UniProt: P04439*PLUS
#2: Protein BETA-2-MICROGLOBULIN / HDCMA22P


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide MELANOMA-ASSOCIATED ANTIGEN 1 / MAGE-A1 / MAGE-1 ANTIGEN / ANTIGEN MZ2-E


Mass: 976.964 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P43355

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Antibody , 2 types, 4 molecules HILM

#4: Antibody HYB3 HEAVY CHAIN


Mass: 23845.672 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT, RESIDUES 1-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
#5: Antibody HYB3 LIGHT CHAIN


Mass: 22523.867 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT, RESIDUES 1-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)

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Non-polymers , 2 types, 657 molecules

#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 653 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsINVOLVED IN THE PRESENTATION OF FOREIGN ANTIGENS TO THE IMMUNE SYSTEM. BETA-2-MICROGLOBULIN IS THE ...INVOLVED IN THE PRESENTATION OF FOREIGN ANTIGENS TO THE IMMUNE SYSTEM. BETA-2-MICROGLOBULIN IS THE BETA-CHAIN OF MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULES.
Has protein modificationY
Sequence detailsN-TERMINAL MET IS A CLONING ARTIFACT FRAGMENT. THE NUMBERING IN CHAINS L,M,H AND I FOLLOW THE ...N-TERMINAL MET IS A CLONING ARTIFACT FRAGMENT. THE NUMBERING IN CHAINS L,M,H AND I FOLLOW THE STANDARD KABAT NUMBERING SCHEME.

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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: 2.1 Å3/Da / Density % sol: 42 %
Description: A DATABASE OF 125 ANTIBODIES WAS USED AS SEARCH MODELS
Crystal growpH: 6.5 / Details: MES PH 6.5, NACL 600MM, 19% PEG3350, 80MM DIOXANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 14, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 78453 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.3 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1DUZ, 7FAB, 2GFB, 2FB4

1duz

7fab

2gfb

2fb4


Resolution: 2.15→120 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.908 / SU B: 12.789 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3961 5 %RANDOM
Rwork0.182 ---
obs0.186 74477 89.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.79 Å2
2---0.38 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.15→120 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12794 0 24 653 13471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02113168
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211317
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.92417902
X-RAY DIFFRACTIONr_angle_other_deg0.819326408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.48251612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.51823.571616
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.947152056
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1691590
X-RAY DIFFRACTIONr_chiral_restr0.0910.21886
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214806
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022748
X-RAY DIFFRACTIONr_nbd_refined0.1930.22257
X-RAY DIFFRACTIONr_nbd_other0.190.211286
X-RAY DIFFRACTIONr_nbtor_refined0.0850.27349
X-RAY DIFFRACTIONr_nbtor_other0.0850.27349
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2677
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.260
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.2162
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.094210390
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.374313091
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.03646071
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.90864811
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 285
Rwork0.219 5293
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)
11.89680.69891.15791.52961.71033.0695-0.0564-0.09310.0705-0.0016-0.0187-0.01050.00050.0150.075-0.0713-0.00140.07740.06510.02380.096518.26427.671111.398
21.5266-0.0979-0.16621.40030.32384.1982-0.1046-0.163-0.0060.16630.20170.0960.0246-0.0301-0.09710.01850.06190.04820.28940.05950.123261.812-0.06472.029
38.02750.0557-3.49721.1781-0.39861.6425-0.15680.1484-0.2169-0.28030.0124-0.23110.1311-0.00980.14440.0207-0.02460.04750.1852-0.03440.206553.92932.805113.272
47.9989-1.30050.49332.0283-0.03612.03530.1210.2373-0.5892-0.2546-0.10460.0760.40670.1302-0.01640.1880.06450.11380.1822-0.04070.112329.4084.11387.385
55.8782-0.69072.97562.19280.09023.6860.0732-0.1688-0.46280.19050.0111-0.34080.31210.2408-0.08430.02770.02090.04180.13970.0460.266441.62614.388117.435
63.1443-1.6182-2.0945.49550.9794.56170.28050.27270.49050.1499-0.05230.475-0.6592-0.4409-0.22820.17580.10880.14410.42780.11810.334643.07519.38677.113
74.44120.03910.74631.21710.06591.26450.0073-0.01540.1555-0.06070.06230.0705-0.0491-0.0792-0.0695-0.0443-0.0270.0565-0.04620.01030.1355-11.19121.739109.365
82.97612.2409-0.10325.1361-0.09232.41780.07810.0354-0.27030.03810.015-0.11360.32820.0578-0.0931-0.0034-0.040.02270.0113-0.04450.1251-4.4420.86106.608
92.29510.5005-0.23924.5345-1.68215.21710.0094-0.3537-0.09120.5761-0.0129-0.01350.1345-0.00580.00350.09830.00980.01870.18760.02170.2805-36.45310.186120.55
104.0554-1.03160.4963.13840.2681.26590.05990.0520.2680.1127-0.1494-0.11320.0904-0.05210.08950.0241-0.02530.07630.13340.05960.2928-42.363-3.033112.442
112.6554-0.934-1.12281.5390.52881.802-0.1022-0.2904-0.08340.11290.1466-0.22380.01370.0601-0.04440.0567-0.01360.020.18090.03540.084787.831-4.53658.066
123.12141.9163-0.70863.3958-0.98392.1393-0.0725-0.12950.1365-0.0635-0.0358-0.0255-0.1193-0.04860.10820.03140.02440.02620.0819-0.05390.070182.56612.82245.832
132.78411.47392.18944.46992.60443.57050.2144-0.3875-0.1020.3552-0.1938-0.21520.03880.1633-0.02060.0783-0.06110.04630.2812-0.01610.1342117.856-0.14349.731
145.2737-1.46191.04332.7193-0.07442.4352-0.16480.03580.1415-0.07620.024-0.1617-0.14140.09060.1408-0.006-0.06730.01690.2029-0.05210.1358119.6127.52835.132
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2D1 - 180
4X-RAY DIFFRACTION2F1 - 9
5X-RAY DIFFRACTION3A181 - 274
6X-RAY DIFFRACTION4D181 - 274
7X-RAY DIFFRACTION5B1 - 99
8X-RAY DIFFRACTION6E1 - 99
9X-RAY DIFFRACTION7H1 - 123
10X-RAY DIFFRACTION8L1 - 109
11X-RAY DIFFRACTION9H124 - 222
12X-RAY DIFFRACTION10L110 - 210
13X-RAY DIFFRACTION11I1 - 123
14X-RAY DIFFRACTION12M1 - 109
15X-RAY DIFFRACTION13I124 - 222
16X-RAY DIFFRACTION14M110 - 210

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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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