[English] 日本語
Yorodumi
- PDB-6atf: HLA-DRB1*1402 in complex with Vimentin59-71 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6atf
TitleHLA-DRB1*1402 in complex with Vimentin59-71
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • MHC class II antigen
  • Vimentin59-71
KeywordsIMMUNE SYSTEM / HLA Class II
Function / homology
Function and homology information


lens fiber cell development / keratin filament binding / intermediate filament organization / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / cellular response to muramyl dipeptide / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity ...lens fiber cell development / keratin filament binding / intermediate filament organization / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / cellular response to muramyl dipeptide / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / structural constituent of eye lens / positive regulation of CD4-positive, alpha-beta T cell activation / astrocyte development / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / Striated Muscle Contraction / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / microtubule organizing center / transport vesicle membrane / intermediate filament / polysaccharide binding / cell leading edge / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Bergmann glial cell differentiation / Generation of second messenger molecules / immunological synapse / PD-1 signaling / positive regulation of collagen biosynthetic process / Caspase-mediated cleavage of cytoskeletal proteins / T cell receptor binding / regulation of mRNA stability / MHC class II antigen presentation / phagocytic vesicle / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / Late endosomal microautophagy / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / nuclear matrix / cellular response to type II interferon / Aggrephagy / peptide antigen assembly with MHC class II protein complex / Chaperone Mediated Autophagy / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peroxisome / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / neuron projection development / Interferon gamma signaling / positive regulation of immune response / double-stranded RNA binding / Downstream TCR signaling / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / early endosome membrane / scaffold protein binding / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / molecular adaptor activity / lysosome / cytoskeleton / endosome membrane / immune response / protein domain specific binding / lysosomal membrane / axon / Golgi membrane / focal adhesion / positive regulation of gene expression / cell surface / extracellular exosome / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Intermediate filament head, DNA-binding domain / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 ...Intermediate filament head, DNA-binding domain / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / HLA class II histocompatibility antigen DR beta chain / HLA class II histocompatibility antigen, DR alpha chain / Vimentin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsScally, S.W. / Ting, Y.T. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
NHMRC, ARC Australia
CitationJournal: Ann. Rheum. Dis. / Year: 2017
Title: Molecular basis for increased susceptibility of Indigenous North Americans to seropositive rheumatoid arthritis.
Authors: Scally, S.W. / Law, S.C. / Ting, Y.T. / Heemst, J.V. / Sokolove, J. / Deutsch, A.J. / Bridie Clemens, E. / Moustakas, A.K. / Papadopoulos, G.K. / Woude, D.V. / Smolik, I. / Hitchon, C.A. / ...Authors: Scally, S.W. / Law, S.C. / Ting, Y.T. / Heemst, J.V. / Sokolove, J. / Deutsch, A.J. / Bridie Clemens, E. / Moustakas, A.K. / Papadopoulos, G.K. / Woude, D.V. / Smolik, I. / Hitchon, C.A. / Robinson, D.B. / Ferucci, E.D. / Bernstein, C.N. / Meng, X. / Anaparti, V. / Huizinga, T. / Kedzierska, K. / Reid, H.H. / Raychaudhuri, S. / Toes, R.E. / Rossjohn, J. / El-Gabalawy, H. / Thomas, R.
History
DepositionAug 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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 2.1Oct 4, 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: HLA class II histocompatibility antigen, DR alpha chain
B: MHC class II antigen
D: HLA class II histocompatibility antigen, DR alpha chain
E: MHC class II antigen
C: Vimentin59-71
F: Vimentin59-71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,88719
Polymers92,8616
Non-polymers2,02613
Water18,3211017
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: MHC class II antigen
C: Vimentin59-71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,62511
Polymers46,4313
Non-polymers1,1948
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-14 kcal/mol
Surface area18600 Å2
MethodPISA
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: MHC class II antigen
F: Vimentin59-71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2628
Polymers46,4313
Non-polymers8325
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-8 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.980, 77.770, 94.540
Angle α, β, γ (deg.)90.00, 109.52, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 4 molecules ADBE

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 21919.594 Da / Num. of mol.: 2 / Fragment: UNP residues 26-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Homo sapiens (human) / References: UniProt: P01903
#2: Protein MHC class II antigen


Mass: 23072.367 Da / Num. of mol.: 2 / Fragment: UNP residues 30-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Homo sapiens (human) / References: UniProt: A0A0A1I7H6

-
Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide Vimentin59-71


Mass: 1438.657 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P08670*PLUS

-
Sugars , 2 types, 4 molecules

#4: 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: 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
#5: 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: 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, 1026 molecules

#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C2H6O2
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1017 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 26% PEG 3350, 0.2M Potassium Nitrate, 0.1M Bis-Tris-Propane pH 7.3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→33.482 Å / Num. obs: 72027 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rpim(I) all: 0.056 / Net I/σ(I): 10.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 10379 / Rpim(I) all: 0.23 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MCY

4mcy


Resolution: 1.9→33.482 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.86
RfactorNum. reflection% reflection
Rfree0.2023 3632 5.04 %
Rwork0.1699 --
obs0.1715 72003 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→33.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6263 0 132 1026 7421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046626
X-RAY DIFFRACTIONf_angle_d0.9139006
X-RAY DIFFRACTIONf_dihedral_angle_d13.952416
X-RAY DIFFRACTIONf_chiral_restr0.037976
X-RAY DIFFRACTIONf_plane_restr0.0041173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.899-1.9240.26511140.23952554X-RAY DIFFRACTION97
1.924-1.95030.24491380.22242590X-RAY DIFFRACTION99
1.9503-1.97820.25151270.20692629X-RAY DIFFRACTION99
1.9782-2.00770.24381380.1942619X-RAY DIFFRACTION100
2.0077-2.03910.23271470.19132627X-RAY DIFFRACTION100
2.0391-2.07250.22091490.19132570X-RAY DIFFRACTION100
2.0725-2.10830.2241560.1862640X-RAY DIFFRACTION100
2.1083-2.14660.2181490.17552599X-RAY DIFFRACTION100
2.1466-2.18790.20841220.17752629X-RAY DIFFRACTION100
2.1879-2.23250.20311440.17682635X-RAY DIFFRACTION100
2.2325-2.2810.20271420.17062606X-RAY DIFFRACTION100
2.281-2.33410.22261390.17232631X-RAY DIFFRACTION100
2.3341-2.39240.22851380.17622631X-RAY DIFFRACTION100
2.3924-2.45710.22581350.18172628X-RAY DIFFRACTION100
2.4571-2.52940.2381380.17792603X-RAY DIFFRACTION100
2.5294-2.6110.21631540.17012636X-RAY DIFFRACTION100
2.611-2.70430.21381370.17762635X-RAY DIFFRACTION100
2.7043-2.81250.19531370.17242617X-RAY DIFFRACTION100
2.8125-2.94040.19231390.17282669X-RAY DIFFRACTION100
2.9404-3.09540.24241260.16822655X-RAY DIFFRACTION100
3.0954-3.28910.191400.16232636X-RAY DIFFRACTION100
3.2891-3.54280.17931340.15452669X-RAY DIFFRACTION100
3.5428-3.89890.17181540.15042622X-RAY DIFFRACTION100
3.8989-4.46190.16131380.13512664X-RAY DIFFRACTION100
4.4619-5.61730.18071360.14432680X-RAY DIFFRACTION100
5.6173-33.48760.18131610.1842697X-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)
12.93740.15470.94811.5101-1.67672.3719-0.02620.0541-0.1246-0.01830.0161-0.01450.0409-0.00990.03150.09350.02860.00630.0835-0.02570.088244.87484.374114.3068
23.46980.13-1.04952.94241.17052.6927-0.04350.2013-0.71210.0450.037-0.18170.45250.139-0.06210.17220.00140.01370.0957-0.03990.207444.4942-5.4391106.3641
31.28680.43790.52562.0372.78646.12520.0271-0.0391-0.13920.1117-0.0979-0.04760.20360.14950.03710.1270.0108-0.01240.12890.0570.124854.82034.9213123.0097
43.21491.04251.31831.45520.48312.0635-0.25520.0680.2383-0.11450.06710.29840.0886-0.19810.17430.1347-0.0450.02710.09010.05170.077727.78391.9457119.2004
52.51431.06770.01040.48070.22022.0489-0.0580.0371-0.0873-0.0561-0.0027-0.02120.1388-0.09630.03410.11730.00680.01130.05660.00880.101129.3496-2.8826117.45
61.6990.6968-1.11592.0348-0.49190.87320.07940.1497-0.27490.1937-0.00550.11090.4523-0.6433-0.09030.2098-0.15240.02460.29580.03490.192617.0165-9.3731119.6624
71.64750.4442-1.72813.23970.16191.92280.0908-0.55050.2290.0965-0.2460.3560.1915-0.61890.20580.08770.0010.04430.24420.02070.116921.2619-0.7732124.9657
81.48420.2826-0.03620.872-0.26741.9618-0.03240.07210.04380.0167-0.0042-0.0407-0.17390.02450.03880.08340.005-0.00430.07990.01150.084751.500214.2851112.2493
93.3862-1.3576-0.00690.90960.19761.24380.02780.2289-0.074-0.0646-0.05010.1312-0.0972-0.11370.02340.1272-0.029-0.00150.1-0.03470.111614.67417.252798.5826
102.32760.6905-0.53930.72180.1296.9659-0.03180.0330.1230.00110.07380.0173-0.18860.1387-0.01240.06010.0131-0.00780.0676-0.00090.080627.834935.3216114.5136
113.6831-0.02030.98763.1217-0.91943.28260.04030.1190.6620.0419-0.04110.1262-0.505-0.0877-0.04280.16030.013-0.0090.08830.03780.192128.206745.1556106.5348
121.37070.3844-0.67122.3568-2.83866.3124-0.0512-0.11050.17840.17430.04870.0811-0.1556-0.2789-0.02440.11410.0120.01670.1287-0.05760.118717.730534.7548123.7334
132.88050.5629-1.34211.3746-0.25921.6637-0.21010.1277-0.2167-0.1240.0065-0.2866-0.05960.14140.20110.1068-0.0427-0.03890.1283-0.01370.056344.911437.7896119.4162
142.5030.7740.01250.5633-0.29771.6464-0.07380.06580.0776-0.0863-0.0070.0076-0.23450.04660.05220.1415-0.0067-0.00670.0659-0.00570.077443.346742.5925117.6392
152.78081.6257-0.23122.9815-0.55022.14830.2056-0.422-0.050.1365-0.2842-0.2508-0.3550.69310.09590.1455-0.0741-0.02010.2504-0.01150.121952.930644122.6793
161.22630.0271-0.02061.12050.26782.2714-0.00640.0203-0.0719-0.01530.0069-0.03170.06320.0538-0.01150.06660.00620.00490.0834-0.00620.076924.622524.9498114.8585
172.47081.1179-1.21331.9143-0.69712.6823-0.05610.2325-0.03530.04390.06040.14010.1647-0.23140.02460.08750.0132-0.00460.0981-0.02960.08216.490426.0611108.9023
183.2446-1.53010.0310.9146-0.27790.92690.04870.30190.1171-0.0514-0.0914-0.14690.07910.09150.03930.1244-0.02530.00460.11820.03160.114157.933132.626398.6132
193.02571.63382.73322.99513.21075.4895-0.0230.1596-0.25370.18480.262-0.30390.07130.403-0.25650.11070.0222-0.01430.10550.01030.114956.27626.7543113.7522
202.13340.7958-1.16521.7834-1.63683.20180.11570.05310.27430.30780.17030.3597-0.2924-0.2484-0.30160.11780.01950.04110.119-0.01140.123616.424332.956113.9199
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 101 )
5X-RAY DIFFRACTION5chain 'A' and (resid 102 through 154 )
6X-RAY DIFFRACTION6chain 'A' and (resid 155 through 166 )
7X-RAY DIFFRACTION7chain 'A' and (resid 167 through 181 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 89 )
9X-RAY DIFFRACTION9chain 'B' and (resid 90 through 190 )
10X-RAY DIFFRACTION10chain 'D' and (resid 3 through 26 )
11X-RAY DIFFRACTION11chain 'D' and (resid 27 through 55 )
12X-RAY DIFFRACTION12chain 'D' and (resid 56 through 76 )
13X-RAY DIFFRACTION13chain 'D' and (resid 77 through 101 )
14X-RAY DIFFRACTION14chain 'D' and (resid 102 through 154 )
15X-RAY DIFFRACTION15chain 'D' and (resid 155 through 181 )
16X-RAY DIFFRACTION16chain 'E' and (resid 2 through 51 )
17X-RAY DIFFRACTION17chain 'E' and (resid 52 through 89 )
18X-RAY DIFFRACTION18chain 'E' and (resid 90 through 190 )
19X-RAY DIFFRACTION19chain 'C' and (resid 1 through 13 )
20X-RAY DIFFRACTION20chain '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://pdbjlvh1.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