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- PDB-4gg6: Protein complex -

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Basic information

Entry
Database: PDB / ID: 4gg6
TitleProtein complex
Components
  • (HLA class II histocompatibility antigen, DQ ...) x 2
  • (T-CELL RECEPTOR, SP3.4 ...) x 2
  • Peptide from Alpha/beta-gliadin MM1
KeywordsIMMUNE SYSTEM / IMMUNE RECEPTOR-LIGAND COMPLEX
Function / homology
Function and homology information


nutrient reservoir activity / MHC class II receptor activity / alpha-beta T cell receptor complex / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / humoral immune response / Generation of second messenger molecules / PD-1 signaling ...nutrient reservoir activity / MHC class II receptor activity / alpha-beta T cell receptor complex / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / humoral immune response / Generation of second messenger molecules / PD-1 signaling / immunoglobulin complex, circulating / immunoglobulin receptor binding / MHC class II antigen presentation / trans-Golgi network membrane / complement activation, classical pathway / lumenal side of endoplasmic reticulum membrane / antigen binding / response to bacterium / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / antibacterial humoral response / adaptive immune response / blood microparticle / immune response / lysosomal membrane / Golgi membrane / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Gliadin/LMW glutenin / Cys-rich Gliadin N-terminal / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / T-cell receptor alpha chain, constant domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Domain of unknown function (DUF1968) / MHC class II, beta chain, N-terminal ...Gliadin/LMW glutenin / Cys-rich Gliadin N-terminal / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / T-cell receptor alpha chain, constant domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Domain of unknown function (DUF1968) / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Immunoglobulin V-Type / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T-cell receptor, sp3.4 alpha chain / T cell receptor beta constant 1 / HLA class II histocompatibility antigen, DQ alpha 1 chain / HLA class II histocompatibility antigen, DQ beta 1 chain / Alpha/beta-gliadin MM1
Similarity search - Component
Biological speciesHomo sapiens (human)
Triticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBroughton, S.E. / Theodossis, A. / Petersen, J. / Reid, H.H. / Rossjohn, J.
CitationJournal: Immunity / Year: 2012
Title: Biased T cell receptor usage directed against human leukocyte antigen DQ8-restricted gliadin peptides is associated with celiac disease.
Authors: Broughton, S.E. / Petersen, J. / Theodossis, A. / Scally, S.W. / Loh, K.L. / Thompson, A. / van Bergen, J. / Kooy-Winkelaar, Y. / Henderson, K.N. / Beddoe, T. / Tye-Din, J.A. / Mannering, S. ...Authors: Broughton, S.E. / Petersen, J. / Theodossis, A. / Scally, S.W. / Loh, K.L. / Thompson, A. / van Bergen, J. / Kooy-Winkelaar, Y. / Henderson, K.N. / Beddoe, T. / Tye-Din, J.A. / Mannering, S.I. / Purcell, A.W. / McCluskey, J. / Anderson, R.P. / Koning, F. / Reid, H.H. / Rossjohn, J.
History
DepositionAug 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Aug 24, 2022Group: Database references / Structure summary / Category: chem_comp / citation / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DQ alpha 1 chain
B: HLA class II histocompatibility antigen, DQ beta 1 chain
C: HLA class II histocompatibility antigen, DQ alpha 1 chain
D: HLA class II histocompatibility antigen, DQ beta 1 chain
E: T-CELL RECEPTOR, SP3.4 ALPHA CHAIN
F: T-CELL RECEPTOR, SP3.4 BETA CHAIN
G: T-CELL RECEPTOR, SP3.4 ALPHA CHAIN
H: T-CELL RECEPTOR, SP3.4 BETA CHAIN
I: Peptide from Alpha/beta-gliadin MM1
J: Peptide from Alpha/beta-gliadin MM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,83713
Polymers198,17410
Non-polymers6643
Water00
1
A: HLA class II histocompatibility antigen, DQ alpha 1 chain
B: HLA class II histocompatibility antigen, DQ beta 1 chain
G: T-CELL RECEPTOR, SP3.4 ALPHA CHAIN
H: T-CELL RECEPTOR, SP3.4 BETA CHAIN
J: Peptide from Alpha/beta-gliadin MM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5297
Polymers99,0875
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HLA class II histocompatibility antigen, DQ alpha 1 chain
D: HLA class II histocompatibility antigen, DQ beta 1 chain
E: T-CELL RECEPTOR, SP3.4 ALPHA CHAIN
F: T-CELL RECEPTOR, SP3.4 BETA CHAIN
I: Peptide from Alpha/beta-gliadin MM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3086
Polymers99,0875
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.708, 134.325, 140.304
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13E
23G
14F
24H
15I
25J
16C
26A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 155
2112C1 - 155
1215A156 - 162
2215C156 - 162
1312A163 - 182
2312C163 - 182
1122B3 - 101
2122D3 - 101
1225B102 - 115
2225D102 - 115
1322B116 - 131
2322D116 - 131
1425B132 - 142
2425D132 - 142
1522B143 - 161
2522D143 - 161
1625B162 - 171
2625D162 - 171
1722B172 - 185
2722D172 - 185
1825B186 - 189
2825D186 - 189
1925B2
2925D2
1132E3 - 127
2132G3 - 127
1235E128 - 131
2235G128 - 131
1332E151 - 180
2332G151 - 180
1435E190 - 201
2435G190 - 201
1532E132 - 143
2532G132 - 143
1635E144 - 150
2635G144 - 150
1732E184 - 189
2732G184 - 189
1835E181 - 183
2835G181 - 183
1142F2 - 244
2142H2 - 244
1152I1 - 13
2152J1 - 13
1162C201
2162A201 - 202

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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HLA class II histocompatibility antigen, DQ ... , 2 types, 4 molecules ACBD

#1: Protein HLA class II histocompatibility antigen, DQ alpha 1 chain / DC-1 alpha chain / DC-alpha / HLA-DCA / MHC class II DQA1


Mass: 21874.377 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS, UNP RESIDUES 24-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Plasmid: PFASTBACDUAL / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): HI5 / References: UniProt: P01909
#2: Protein HLA class II histocompatibility antigen, DQ beta 1 chain / MHC class II antigen DQB1


Mass: 24606.475 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS, UNP RESIDUES 33-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB, HLA-DQB1 / Plasmid: PFASTBACDUAL / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): HI5 / References: UniProt: P01920

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T-CELL RECEPTOR, SP3.4 ... , 2 types, 4 molecules EGFH

#3: Protein T-CELL RECEPTOR, SP3.4 ALPHA CHAIN


Mass: 23039.484 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS / Mutation: T176C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: K7N5N2*PLUS
#4: Protein T-CELL RECEPTOR, SP3.4 BETA CHAIN


Mass: 27558.459 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS / Mutation: C202A, S184C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01850*PLUS

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Protein/peptide / Sugars , 2 types, 5 molecules IJ

#5: Protein/peptide Peptide from Alpha/beta-gliadin MM1 / Prolamin


Mass: 2008.019 Da / Num. of mol.: 2
Fragment: DEAMIDATED ALPHA-I GLIADIN PEPTIDE, UNP RESIDUES 243-260
Mutation: Q3E, Q11E / Source method: obtained synthetically / Details: CHEMICAL SYNTHESIS / Source: (synth.) Triticum aestivum (bread wheat) / References: UniProt: P18573
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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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Details

Sequence details1. SEQUENCE CONFLICTS OF ENTITY 1 AND 2 ARE ALL NATURAL VARIANTS ACCORDING TO DATABASE UNIPROT ...1. SEQUENCE CONFLICTS OF ENTITY 1 AND 2 ARE ALL NATURAL VARIANTS ACCORDING TO DATABASE UNIPROT P01909 (ENTITY 1) AND P01920 (ENTITY 2) RESPECTIVELY. 2. RESIDUES NUMBERING FOR CHAIN A,C,E,G,F AND H HAVE BEEN CHANGED TO CONFORM WITH THE NUMBERING CONVENTION IN THE IMGT DATABASE. 3. THE SEQUENCE DATABASE FOR ENTITY 3 AND 4 CURRENTLY DO NOT EXIST. ACCORDING TO AUTHOR, RESIDUE 176 (T176C) IN ENTITY 3 AND RESIDUES 184 (S184C) AND 202 (C202A) IN ENTITY 4 ARE ENGINEERED MUTATIONS.

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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: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M SODIUM ACETATE, 0.1M MES PH 6.5, 17% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95666 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95666 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. obs: 32429 / % possible obs: 91 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.173 / Net I/σ(I): 9.1
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2.6 / % possible all: 93.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1KGC AND 2NNA

1kgc

2nna


Resolution: 3.2→35.88 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.837 / SU B: 59.408 / SU ML: 0.445 / Cross valid method: THROUGHOUT / ESU R Free: 0.597 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1646 5.1 %RANDOM
Rwork0.246 ---
obs0.248 30631 91 %-
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: 43.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å20 Å2
2--0.61 Å2-0 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 3.2→35.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11877 0 42 0 11919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02112251
X-RAY DIFFRACTIONr_angle_refined_deg0.9751.93916794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.31151549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1323.816532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.191151627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6651558
X-RAY DIFFRACTIONr_chiral_restr0.0620.21905
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219539
X-RAY DIFFRACTIONr_mcbond_it0.1151.57852
X-RAY DIFFRACTIONr_mcangle_it0.224212533
X-RAY DIFFRACTIONr_scbond_it0.36234399
X-RAY DIFFRACTIONr_scangle_it0.6214.54261
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A700tight positional0.020.05
2B592tight positional0.30.05
3E692tight positional0.020.05
4F972tight positional0.020.05
5I52tight positional0.140.05
1A662medium positional0.020.5
2B612medium positional0.390.5
3E594medium positional0.030.5
4F833medium positional0.020.5
5I44medium positional0.320.5
6C14medium positional0.140.5
1A7loose positional0.025
2B30loose positional1.065
3E4loose positional0.025
1A700tight thermal0.020.5
2B592tight thermal0.110.5
3E692tight thermal0.020.5
4F972tight thermal0.020.5
5I52tight thermal0.080.5
1A662medium thermal0.032
2B612medium thermal0.182
3E594medium thermal0.032
4F833medium thermal0.032
5I44medium thermal0.192
6C14medium thermal0.092
1A7loose thermal0.0210
2B30loose thermal0.1310
3E4loose thermal0.0210
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 113 -
Rwork0.324 2276 -
obs--93.5 %
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)
16.4179-0.17731.20321.6710.13961.0184-0.0524-0.1949-0.1689-0.06410.05650.08660.1088-0.1312-0.00410.2132-0.00930.04840.1307-0.01510.1314-73.36167.975-43.861
22.45780.74270.0323.42192.68566.9454-0.09160.1003-0.40710.2871-0.1290.48120.7783-0.94090.22060.3616-0.0336-0.00640.5127-0.02250.3976-94.85664.634-59.594
33.40121.48163.38453.26261.80923.43090.16090.4975-0.1569-0.1188-0.01-0.30150.11880.4265-0.15090.23820.00360.02390.38920.0150.1496-61.43169.035-63.778
43.1219-1.2522-2.73231.79642.37856.47250.01650.3583-0.0587-0.2701-0.17850.2578-0.2712-0.37880.1620.2765-0.0056-0.05830.1942-0.02910.1556-88.89170.644-72.204
55.01360.41240.65141.9588-0.54321.44310.0463-0.44130.15770.0301-0.1402-0.2772-0.0930.35160.09380.2311-0.0174-0.05340.22020.09910.328917.40830.606-36.423
62.51880.61960.3621.6943-0.16182.4628-0.1573-0.17930.47030.23480.0183-0.7944-0.55860.76660.13910.5619-0.0440.02310.74080.04260.743837.88632.703-50.12
74.95841.2534-3.55012.0197-1.20564.0985-0.01510.66020.1128-0.27460.0585-0.0185-0.0624-0.1423-0.04330.3098-0.06120.01620.28370.05520.22995.60728.84-56.552
85.0128-1.16951.38132.3357-1.62263.8113-0.0080.9690.0102-0.3565-0.4844-0.45670.34470.60430.49240.47530.1310.19590.52020.17720.422133.0827.647-64.612
92.96990.38340.21383.5939-0.57932.0590.0696-0.04280.24950.1748-0.0087-0.0331-0.21910.0522-0.06090.13180.02010.04850.13220.1010.1167-13.16523.967-31.998
102.6436-1.3456-0.64494.02550.29811.04620.37510.0630.192-0.2361-0.06720.7926-0.5212-0.5062-0.30790.39160.14540.14550.39880.210.4671-38.53131.228-32.69
110.5429-0.2553-1.45761.66072.67467.11760.3701-0.14270.4490.26970.23580.1436-0.39030.0509-0.60590.76730.15990.38020.6571-0.23070.7236-35.05638.16-10.256
121.89360.5540.33792.92740.05510.6695-0.0713-0.08750.16120.07770.12610.0544-0.00070.0028-0.05480.12350.0254-0.03180.2202-0.10030.1901-42.42274.203-39.62
130.592-0.8543-0.32464.0517-0.70080.6673-0.0522-0.18310.1256-0.271-0.2124-0.95630.15450.31080.26470.2233-0.0132-0.00530.4729-0.11090.5103-16.66867.373-41.009
145.284-0.65084.0780.5154-0.86244.15250.4142-0.2532-0.15820.2767-0.1097-0.24520.13140.494-0.30450.45010.0223-0.19760.5676-0.19070.4385-17.57659.349-17.683
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E3 - 113
2X-RAY DIFFRACTION2E114 - 201
3X-RAY DIFFRACTION3F2 - 117
4X-RAY DIFFRACTION4F118 - 244
5X-RAY DIFFRACTION5G3 - 113
6X-RAY DIFFRACTION6G114 - 189
7X-RAY DIFFRACTION7H2 - 117
8X-RAY DIFFRACTION8H118 - 244
9X-RAY DIFFRACTION9A1 - 85
10X-RAY DIFFRACTION9B3 - 92
11X-RAY DIFFRACTION9J1 - 13
12X-RAY DIFFRACTION9A201
13X-RAY DIFFRACTION10A86 - 180
14X-RAY DIFFRACTION10A202
15X-RAY DIFFRACTION11B93 - 188
16X-RAY DIFFRACTION12C1 - 85
17X-RAY DIFFRACTION12D2 - 92
18X-RAY DIFFRACTION12I1 - 13
19X-RAY DIFFRACTION13C86 - 180
20X-RAY DIFFRACTION13C201
21X-RAY DIFFRACTION14D93 - 189

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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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