[English] 日本語
Yorodumi
- PDB-6xp6: 3C11-DQ2-glia-a2 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xp6
Title3C11-DQ2-glia-a2 complex
Components
  • (MHC class II HLA-DQ- ...) x 2
  • 3.C11 IgH Fab
  • 3.C11 IgK Fab
  • DQ2-glia-a2 peptide
KeywordsPEPTIDE BINDING PROTEIN / Complex Antibody Human Leucocyte Antigen
Function / homology
Function and homology information


antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / endosome membrane / lysosomal membrane
Similarity search - Function
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 / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site ...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 / 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 / Mainly Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / MHC class II HLA-DQ-alpha chain / MHC class II HLA-DQ-beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Triticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPetersen, J. / Rossjohn, J.
CitationJournal: Sci Immunol / Year: 2021
Title: A high-affinity human TCR-like antibody detects celiac disease gluten peptide-MHC complexes and inhibits T cell activation.
Authors: Frick, R. / Hoydahl, L.S. / Petersen, J. / du Pre, M.F. / Kumari, S. / Berntsen, G. / Dewan, A.E. / Jeliazkov, J.R. / Gunnarsen, K.S. / Frigstad, T. / Vik, E.S. / Llerena, C. / Lundin, K.E.A. ...Authors: Frick, R. / Hoydahl, L.S. / Petersen, J. / du Pre, M.F. / Kumari, S. / Berntsen, G. / Dewan, A.E. / Jeliazkov, J.R. / Gunnarsen, K.S. / Frigstad, T. / Vik, E.S. / Llerena, C. / Lundin, K.E.A. / Yaqub, S. / Jahnsen, J. / Gray, J.J. / Rossjohn, J. / Sollid, L.M. / Sandlie, I. / Loset, G.A.
History
DepositionJul 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MHC class II HLA-DQ-alpha chain
B: MHC class II HLA-DQ-beta-1
D: MHC class II HLA-DQ-alpha chain
E: MHC class II HLA-DQ-beta-1
H: 3.C11 IgH Fab
J: 3.C11 IgH Fab
G: 3.C11 IgK Fab
I: 3.C11 IgK Fab
C: DQ2-glia-a2 peptide
F: DQ2-glia-a2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,97532
Polymers188,66610
Non-polymers4,30922
Water14,682815
1
A: MHC class II HLA-DQ-alpha chain
B: MHC class II HLA-DQ-beta-1
H: 3.C11 IgH Fab
G: 3.C11 IgK Fab
C: DQ2-glia-a2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,70918
Polymers94,3335
Non-polymers2,37613
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: MHC class II HLA-DQ-alpha chain
E: MHC class II HLA-DQ-beta-1
J: 3.C11 IgH Fab
I: 3.C11 IgK Fab
F: DQ2-glia-a2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,26714
Polymers94,3335
Non-polymers1,9339
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.847, 143.047, 170.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
MHC class II HLA-DQ- ... , 2 types, 4 molecules ADBE

#1: Protein MHC class II HLA-DQ-alpha chain


Mass: 21517.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O19705
#2: Protein MHC class II HLA-DQ-beta-1


Mass: 23374.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O19712

-
Protein/peptide , 1 types, 2 molecules CF

#5: Protein/peptide DQ2-glia-a2 peptide


Mass: 2438.587 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Production host: Trichoplusia ni (cabbage looper)

-
Antibody , 2 types, 4 molecules HJGI

#3: Antibody 3.C11 IgH Fab


Mass: 23575.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Antibody 3.C11 IgK Fab


Mass: 23426.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

-
Sugars , 4 types, 6 molecules

#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.: 3 / 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
#7: Polysaccharide beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1203.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpb1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3-3-3-2/a3-b1_a4-c1_a6-g1_c4-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#8: Polysaccharide beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-6)-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
DManpb1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#9: 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.: 1 / 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

-
Non-polymers , 3 types, 831 molecules

#10: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C3H8O
#11: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 815 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 4000 20% 2-propanol 0.1M HEPES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.4→47.03 Å / Num. obs: 88213 / % possible obs: 99.93 % / Redundancy: 2 % / CC1/2: 0.993 / Rpim(I) all: 0.07157 / Net I/σ(I): 8.78
Reflection shellResolution: 2.4→2.486 Å / Num. unique obs: 8724 / CC1/2: 0.633 / Rpim(I) all: 0.5562

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5jo4, 6mfg

5jo4

6mfg


Resolution: 2.4→47.03 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2124 1831 2.08 %
Rwork0.1762 --
obs0.177 88192 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12511 0 281 815 13607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613176
X-RAY DIFFRACTIONf_angle_d0.83117946
X-RAY DIFFRACTIONf_dihedral_angle_d19.1844840
X-RAY DIFFRACTIONf_chiral_restr0.0532072
X-RAY DIFFRACTIONf_plane_restr0.0062282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.31041420.27466571X-RAY DIFFRACTION100
2.46-2.540.27481470.24716559X-RAY DIFFRACTION100
2.54-2.620.31341560.24176561X-RAY DIFFRACTION100
2.62-2.710.30951320.23146560X-RAY DIFFRACTION100
2.71-2.820.25831270.22466578X-RAY DIFFRACTION100
2.82-2.950.26321430.21786602X-RAY DIFFRACTION100
2.95-3.110.26511470.19726593X-RAY DIFFRACTION100
3.11-3.30.221310.18086629X-RAY DIFFRACTION100
3.3-3.550.18771470.16956623X-RAY DIFFRACTION100
3.55-3.910.19821500.15286635X-RAY DIFFRACTION100
3.91-4.480.15271460.13066718X-RAY DIFFRACTION100
4.48-5.640.14231120.1326750X-RAY DIFFRACTION100
5.64-47.030.20751510.17736982X-RAY DIFFRACTION100
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)
11.2485-1.450.59084.2459-1.36254.6077-0.1054-0.02770.09720.24280.0152-0.2618-0.2970.15250.12420.3605-0.0845-0.0320.2292-0.04550.2878-0.2655-27.1895-13.5919
27.1483-6.34684.50848.9319-7.07527.6980.2385-0.243-0.43930.14820.22711.16890.1642-0.2648-0.51090.373-0.05290.02890.2427-0.00630.4084-13.0603-29.8807-14.6139
31.8287-0.1810.32284.28021.08132.1708-0.0966-0.07740.09070.67370.2247-0.61390.37930.4359-0.16130.48430.0359-0.14180.3636-0.07370.36639.1671-36.2293-5.6852
44.3976-4.5886-1.34026.97641.78942.59320.0983-0.24190.09220.37060.1703-0.13070.0240.0454-0.2450.4223-0.0795-0.00550.2676-0.04580.2422-5.3518-10.5413-1.0991
53.5529-3.5834-2.21725.51.54942.4672-0.0968-0.23270.22290.37840.3748-0.37340.07870.0328-0.2980.3638-0.0288-0.0010.2829-0.04940.2573-3.3121-12.7925-2.5299
63.96060.4565-0.31132.05083.10424.9645-0.8667-0.50891.12931.5170.7959-1.6005-0.45760.47880.16790.5529-0.0566-0.08890.3883-0.15340.45281.9744-8.55434.6392
71.431-1.4583-0.15014.01960.67481.47350.130.0823-0.1302-0.16790.0663-0.29450.03620.2293-0.19930.3029-0.06090.02220.3018-0.05950.31086.9297-31.5146-21.761
83.66670.960.63998.98830.04843.1530.01890.03370.3912-0.2958-0.03970.1195-0.3869-0.06640.020.3924-0.02760.06580.2823-0.02260.2296-4.46884.9557-20.8388
92.21831.60071.78484.55551.67783.4546-0.0420.0766-0.1417-0.05650.1244-0.33020.1850.1562-0.09890.3040.0229-0.02320.21070.00990.258720.360838.0112-22.5186
109.19342.6378-6.95232.4879-2.22695.33440.5386-0.33090.28570.2719-0.10730.115-1.06430.1123-0.43130.32490.0221-0.04340.22270.00850.249716.002450.7458-11.8709
111.6857-1.9819-0.63056.94332.37583.5969-0.0722-0.0907-0.36110.56370.02210.3270.38890.18970.07940.32730.0166-0.01340.30190.06720.249320.985321.9393-10.9849
124.1154-1.6856-1.38944.20011.34623.4337-0.2521-0.3966-0.24280.79920.3688-0.32330.44260.4646-0.11950.5309-0.01-0.05780.28530.04390.388325.76222.2759-8.4387
131.5154-1.2411-0.34123.86090.25421.14610.10570.0593-0.0708-0.1519-0.06210.3593-0.1306-0.1926-0.0190.2238-0.0368-0.01250.26230.02450.2886.626342.37-22.2257
143.91652.535-0.8658.6830.0352.3785-0.1213-0.0357-0.42350.0575-0.0837-0.11860.5059-0.06590.17590.32550.01080.02380.2263-0.00280.187114.4077.7943-24.9728
154.8617-0.51990.65746.4909-1.15011.304-0.10170.0401-0.8521-0.18790.1120.35741.00230.4295-0.03850.74230.08670.08810.3112-0.0610.424515.47370.0128-31.877
169.52725.01370.00257.50430.29620.7895-0.1315-0.6569-0.92860.8203-0.1142-0.20710.64860.19490.25640.6960.0464-0.0040.32410.04120.2586-8.3436-66.6795-5.3547
175.19553.7034-5.68443.5822-5.32678.0340.5401-0.7441-0.25071.1189-0.6071-0.4127-0.46720.38280.0180.63830.0432-0.07390.3784-0.00080.44152.9325-56.0937-7.8774
182.863.0098-0.93356.89221.61462.66710.2736-0.31960.35510.8902-0.29280.69410.1864-0.03220.04680.63020.0260.11220.3301-0.01420.3336-12.107-56.2822-7.3246
192.5272.5259-0.82895.5881-1.10910.23730.08020.1657-0.08870.19670.04310.1286-0.0717-0.1002-0.13020.48950.03370.05290.30390.00030.2624-14.5517-72.0232-15.9911
204.06491.99780.51715.72614.79739.2397-0.2140.0785-0.4470.13940.1441-0.51230.04440.16650.12040.431-0.03180.06710.2230.02860.4542-18.9679-89.4505-17.2997
212.95251.0215-1.04394.0472.10388.3652-0.04360.2859-0.58580.13120.0845-0.360.55210.0557-0.01460.3583-0.00880.10.29220.02240.5505-19.5506-92.1148-19.4657
227.15244.7428-6.22827.6618-3.02966.03390.0423-0.51041.42210.50860.07160.1865-0.61360.2051-0.11830.4232-0.0451-0.1020.2874-0.05050.255630.720176.1064-18.3508
234.37452.05110.20183.4068-0.78191.6049-0.041-0.0201-0.02520.1455-0.0554-0.1966-0.25310.17270.07920.3299-0.0124-0.04250.2195-0.01170.198827.506166.1641-20.8765
241.90960.3242-0.91754.53-1.75832.480.18180.30450.64690.2398-0.2858-0.3891-1.20040.43650.17920.7565-0.1043-0.04010.44430.10010.65436.817393.7313-36.151
256.1634-1.8881.79128.86650.10941.85730.07780.32471.24860.7704-0.4414-0.3946-1.47730.66730.36131.0046-0.0909-0.00450.50950.08230.861835.472102.7684-40.4377
266.5698-4.4526-4.61844.03115.65929.68310.07590.28950.2664-0.1439-0.18540.21740.2151-0.67690.17150.40580.00980.00520.30950.00880.3514-15.0126-58.981-33.9614
272.4053-0.1585-0.75172.29241.77125.4271-0.0076-0.01390.2632-0.0955-0.10140.0028-0.268-0.09110.12340.3107-0.0042-0.0170.19330.02750.2488-7.5628-55.3602-29.1751
285.85896.98415.42488.33076.42285.02740.02160.5225-0.9964-0.05480.4428-0.71580.7081-0.1873-0.46550.4079-0.05520.00130.4218-0.06920.3997-17.294-74.4925-39.3283
298.73592.5261-3.8265.7351-1.04855.59380.1678-0.00820.29370.1869-0.05690.5697-0.1591-0.7139-0.13260.3258-0.0455-0.01120.39820.00610.3083-32.0348-82.7794-24.8195
304.99573.2391-3.76584.2623-2.7675.9824-0.06270.74250.4487-0.16850.50970.6287-0.0514-0.8603-0.44410.3377-0.02560.00920.40670.09250.4107-32.4123-82.9797-28.1596
312.803-1.46240.31554.4071-0.6263.5430.08220.2558-0.0621-0.4161-0.0926-0.04-0.0050.0780.01080.2806-0.0202-0.02270.2132-0.02670.186816.301765.891-38.3021
325.0984.3069-1.46634.8494-0.29298.1624-1.00761.63840.9267-0.8321.09080.4263-1.481-0.1118-0.09910.7139-0.0808-0.06250.76330.17990.462319.211382.6202-51.874
332.29030.0574-1.09283.7569-1.76933.99590.08090.5593-0.1976-0.108-0.3355-0.8043-0.28530.75510.28680.6101-0.07220.07610.70770.09610.691340.911487.4127-49.2073
344.99182.07680.11194.9465-2.09684.0146-0.08341.2886-0.9496-0.43540.0587-0.6932-0.080.72640.06560.5108-0.01720.07990.8196-0.04080.630239.085287.3415-51.8881
359.1426-8.44521.25598.9947-2.81222.4036-0.40460.4077-0.14320.2850.1804-0.0808-0.54560.4840.26190.407-0.0839-0.05280.3461-0.08040.35212.8745-39.2568-18.1341
368.333-4.7216-5.95965.90264.46874.59950.20180.77930.2009-0.3035-0.0991-0.02720.3119-0.9336-0.31570.4531-0.0475-0.00840.30060.05690.252212.544249.7672-21.6984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 134 )
5X-RAY DIFFRACTION5chain 'A' and (resid 135 through 166 )
6X-RAY DIFFRACTION6chain 'A' and (resid 167 through 181 )
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 97 )
8X-RAY DIFFRACTION8chain 'B' and (resid 98 through 190 )
9X-RAY DIFFRACTION9chain 'D' and (resid 0 through 55 )
10X-RAY DIFFRACTION10chain 'D' and (resid 56 through 76 )
11X-RAY DIFFRACTION11chain 'D' and (resid 77 through 110 )
12X-RAY DIFFRACTION12chain 'D' and (resid 111 through 181 )
13X-RAY DIFFRACTION13chain 'E' and (resid 3 through 97 )
14X-RAY DIFFRACTION14chain 'E' and (resid 98 through 162 )
15X-RAY DIFFRACTION15chain 'E' and (resid 163 through 190 )
16X-RAY DIFFRACTION16chain 'H' and (resid 2 through 18 )
17X-RAY DIFFRACTION17chain 'H' and (resid 19 through 37 )
18X-RAY DIFFRACTION18chain 'H' and (resid 38 through 99 )
19X-RAY DIFFRACTION19chain 'H' and (resid 100 through 150 )
20X-RAY DIFFRACTION20chain 'H' and (resid 151 through 173 )
21X-RAY DIFFRACTION21chain 'H' and (resid 174 through 229 )
22X-RAY DIFFRACTION22chain 'J' and (resid 2 through 18 )
23X-RAY DIFFRACTION23chain 'J' and (resid 19 through 122 )
24X-RAY DIFFRACTION24chain 'J' and (resid 123 through 191 )
25X-RAY DIFFRACTION25chain 'J' and (resid 192 through 229 )
26X-RAY DIFFRACTION26chain 'G' and (resid 1 through 18 )
27X-RAY DIFFRACTION27chain 'G' and (resid 19 through 118 )
28X-RAY DIFFRACTION28chain 'G' and (resid 119 through 129 )
29X-RAY DIFFRACTION29chain 'G' and (resid 130 through 179 )
30X-RAY DIFFRACTION30chain 'G' and (resid 180 through 228 )
31X-RAY DIFFRACTION31chain 'I' and (resid 1 through 118 )
32X-RAY DIFFRACTION32chain 'I' and (resid 119 through 129 )
33X-RAY DIFFRACTION33chain 'I' and (resid 130 through 179 )
34X-RAY DIFFRACTION34chain 'I' and (resid 180 through 228 )
35X-RAY DIFFRACTION35chain 'C' and (resid 1 through 13 )
36X-RAY DIFFRACTION36chain 'F' and (resid 1 through 13 )

+
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