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- PDB-6ati: HLA-DRB1*1402 in complex with Vimentin-64Cit59-71 -

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Basic information

Entry
Database: PDB / ID: 6ati
TitleHLA-DRB1*1402 in complex with Vimentin-64Cit59-71
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • MHC class II antigen
  • Vimentin-64Cit59-71
KeywordsIMMUNE SYSTEM / HLA Class II
Function / homology
Function and homology information


keratin filament binding / lens fiber cell development / 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 / structural constituent of eye lens ...keratin filament binding / lens fiber cell development / 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 / structural constituent of eye lens / MHC class II receptor activity / 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 / intermediate filament cytoskeleton / Striated Muscle Contraction / intermediate filament / RHOBTB1 GTPase cycle / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / cell leading edge / Bergmann glial cell differentiation / polysaccharide binding / microtubule organizing center / positive regulation of collagen biosynthetic process / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / Caspase-mediated cleavage of cytoskeletal proteins / T cell receptor binding / phagocytic vesicle / regulation of mRNA stability / MHC class II antigen presentation / trans-Golgi network membrane / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / Late endosomal microautophagy / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / cellular response to type II interferon / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / cognition / nuclear matrix / Chaperone Mediated Autophagy / neuron projection development / Interferon gamma signaling / Aggrephagy / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / peroxisome / Downstream TCR signaling / double-stranded RNA binding / negative regulation of neuron projection development / cellular response to lipopolysaccharide / scaffold protein binding / early endosome membrane / Interleukin-4 and Interleukin-13 signaling / molecular adaptor activity / adaptive immune response / cytoskeleton / lysosome / endosome membrane / immune response / protein domain specific binding / Golgi membrane / axon / lysosomal membrane / focal adhesion / positive regulation of gene expression / cell surface / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
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 ...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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen DR beta chain / HLA class II histocompatibility antigen, DR alpha chain / Vimentin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsScally, S.W. / Ting, Y.T. / Rossjohn, J.
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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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, DR alpha chain
B: MHC class II antigen
D: HLA class II histocompatibility antigen, DR alpha chain
E: MHC class II antigen
C: Vimentin-64Cit59-71
F: Vimentin-64Cit59-71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,74610
Polymers92,8616
Non-polymers8854
Water16,141896
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: MHC class II antigen
C: Vimentin-64Cit59-71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8735
Polymers46,4313
Non-polymers4422
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-19 kcal/mol
Surface area18450 Å2
MethodPISA
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: MHC class II antigen
F: Vimentin-64Cit59-71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8735
Polymers46,4313
Non-polymers4422
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-20 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.270, 76.870, 94.910
Angle α, β, γ (deg.)90.00, 109.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#3: Protein/peptide Vimentin-64Cit59-71


Mass: 1438.634 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P08670*PLUS
#4: 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.: 4 / Source method: isolated from a natural 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 896 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.57 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / 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: 1.98→33.629 Å / Num. obs: 63444 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rpim(I) all: 0.056 / Net I/σ(I): 9.1
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 4.3 / Num. unique obs: 9163 / Rpim(I) all: 0.195 / % possible all: 99.3

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Processing

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

4mcy


Resolution: 1.98→33.629 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.76
RfactorNum. reflection% reflection
Rfree0.2333 3210 5.07 %
Rwork0.1898 --
obs0.192 63283 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.98→33.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6268 0 56 901 7225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046524
X-RAY DIFFRACTIONf_angle_d0.8858869
X-RAY DIFFRACTIONf_dihedral_angle_d13.1692361
X-RAY DIFFRACTIONf_chiral_restr0.037962
X-RAY DIFFRACTIONf_plane_restr0.0041157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.00960.2391360.18762533X-RAY DIFFRACTION98
2.0096-2.0410.24851300.19462605X-RAY DIFFRACTION100
2.041-2.07440.34821500.28272569X-RAY DIFFRACTION99
2.0744-2.11020.25581380.21862599X-RAY DIFFRACTION100
2.1102-2.14850.23461310.18782610X-RAY DIFFRACTION100
2.1485-2.18990.23871310.19062632X-RAY DIFFRACTION100
2.1899-2.23450.30191470.23932580X-RAY DIFFRACTION99
2.2345-2.28310.42971340.37472505X-RAY DIFFRACTION97
2.2831-2.33620.22891610.19512614X-RAY DIFFRACTION100
2.3362-2.39460.24041260.19222628X-RAY DIFFRACTION100
2.3946-2.45940.20751320.18592618X-RAY DIFFRACTION100
2.4594-2.53170.24321380.18572600X-RAY DIFFRACTION100
2.5317-2.61340.25011660.18772621X-RAY DIFFRACTION100
2.6134-2.70680.22621270.19552622X-RAY DIFFRACTION100
2.7068-2.81510.251280.17962619X-RAY DIFFRACTION100
2.8151-2.94310.21261470.18362616X-RAY DIFFRACTION100
2.9431-3.09820.21871550.17882619X-RAY DIFFRACTION100
3.0982-3.29210.21711200.17532647X-RAY DIFFRACTION100
3.2921-3.54610.19371350.16322618X-RAY DIFFRACTION100
3.5461-3.90250.23321520.17312622X-RAY DIFFRACTION100
3.9025-4.4660.16311420.14262633X-RAY DIFFRACTION100
4.466-5.62250.17991440.14832662X-RAY DIFFRACTION100
5.6225-33.63390.22891400.1972701X-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)
11.06010.549-0.43810.3307-0.46021.75760.03940.03380.14730.08310.03760.0784-0.14540.0555-0.02850.0940.01570.00880.07380.00210.1067-39.10550.0061112.7153
21.6214-1.07740.44112.0511-0.19761.68740.07260.37060.519-0.1447-0.0724-0.3187-0.2394-0.06090.1490.17420.0813-0.01840.21540.12460.2479-40.10837.2113101.0186
31.33890.1147-0.02952.0693-1.58683.13210.0443-0.12790.2040.0411-0.02270.2471-0.0903-0.22640.01070.14170.00870.02030.1111-0.04370.1118-49.6192-4.2995123.9769
43.74870.2969-1.75820.10970.0341.34650.038-0.1741-0.01690.1214-0.0828-0.07050.0162-0.01850.06080.10710.020.01140.07990.03910.1074-35.9023-10.302132.5161
51.63030.1052-0.29511.674-0.46112.7188-0.27720.23250.1583-0.36030.199-0.21-0.0540.13840.0270.178-0.05060.00520.2295-0.01510.1968-12.28815.5619109.7946
61.05250.6464-0.51210.5915-0.41061.0058-0.0199-0.00170.06570.0314-0.01140.0117-0.0520.0630.02710.1242-0.0026-0.01320.06980.00060.0938-22.88712.4495120.1782
71.29080.21490.57960.450.14181.063-0.13340.18180.0619-0.09220.05310.2542-0.15570.0770.05590.1171-0.0005-0.00120.07480.00070.1206-26.22382.7544118.2998
80.8149-0.238-0.3490.7299-0.17561.13780.0479-0.03590.22840.05910.0233-0.1054-0.15860.1467-0.04050.1855-0.0380.00650.1157-0.01370.139-17.39637.4127115.0413
91.22090.72420.04061.2878-0.39830.61210.1493-0.45120.04880.1154-0.1451-0.0727-0.02030.34620.04530.159-0.0447-0.01620.1919-0.02760.1144-16.28462.4545124.6195
100.95560.3476-0.20310.7149-0.08020.8842-0.03080.13790.0098-0.01270.03330.05190.1303-0.0778-0.01510.07290.01510.00290.0969-0.00350.0901-46.3219-13.5975112.5581
111.8735-0.7327-0.22180.8244-0.15911.00630.03680.23730.0625-0.0579-0.1065-0.17420.05680.13650.05160.1061-0.00380.00490.13180.03430.1295-9.3379-6.653698.9496
121.43730.21810.15040.64180.15132.0256-0.00560.1523-0.2378-0.072-0.0218-0.11660.29060.07770.0570.10120.0229-0.00820.0892-0.0280.1459-22.8496-40.0802110.3617
131.13360.16670.08282.26151.89583.26390.0411-0.1111-0.240.0386-0.0917-0.19880.07290.18660.03060.13570.0216-0.01620.13740.04950.1557-12.6161-34.3416123.8958
141.9550.5271.09540.83910.25771.5047-0.12910.08040.1266-0.07460.04150.18240.0767-0.07350.05170.116-0.00060.01890.1060.02210.0879-39.7578-37.0848119.576
151.0780.1048-0.01420.33080.30080.9524-0.00090.0326-0.03630.0105-0.0327-0.12290.1015-0.04790.02730.11730.00630.00510.0645-0.00260.1146-38.2048-41.9362117.8734
163.04221.40221.64021.45791.04442.11150.0042-0.50270.02020.0713-0.2030.18650.1213-0.5320.12960.1434-0.0460.01910.16710.00760.1565-47.6717-42.9924122.8989
170.97370.16070.05990.5663-0.1732.34520.00340.0336-0.0019-0.00510.1266-0.0142-0.0512-0.2503-0.19940.09210.0177-0.00990.09530.01280.1056-20.9535-27.2585114.208
181.26650.2545-0.09050.7371-0.2140.8395-0.06880.09390.01010.02680.0228-0.0076-0.11270.12370.04720.07660.0078-0.00080.08280.00920.079-12.761-23.5691111.722
192.1178-0.76850.03971.18920.3111.0283-0.068-0.115-0.01560.08280.00580.1413-0.0031-0.02980.03490.1213-0.01440.00710.1347-0.03860.0931-51.655-33.5556100.1849
201.8836-0.3793-0.12270.8480.28870.66730.07620.14080.0386-0.111-0.1050.1181-0.0657-0.1314-0.00450.1029-0.00650.00460.1233-0.01930.1137-49.979-29.8886102.5154
211.3338-0.5521-0.5260.36680.32330.58630.06310.7307-0.1565-0.1221-0.10950.1805-0.0275-0.32880.0770.1473-0.0138-0.01060.2531-0.0690.1291-57.2397-31.338192.9271
221.04970.5181-0.16552.0754-0.77932.04530.03990.09480.19210.1281-0.0540.3626-0.1746-0.1802-0.38280.07860.04660.01150.09240.02010.151-51.1724-6.3076114.0171
230.60580.77810.53921.52131.69932.4202-0.00590.0463-0.12060.1929-0.0009-0.23770.26190.1569-0.0290.13160.0367-0.02860.101-0.02250.1471-11.034-32.3731113.9223
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 87 )
5X-RAY DIFFRACTION5chain 'A' and (resid 88 through 102 )
6X-RAY DIFFRACTION6chain 'A' and (resid 103 through 123 )
7X-RAY DIFFRACTION7chain 'A' and (resid 124 through 144 )
8X-RAY DIFFRACTION8chain 'A' and (resid 145 through 160 )
9X-RAY DIFFRACTION9chain 'A' and (resid 161 through 181 )
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 89 )
11X-RAY DIFFRACTION11chain 'B' and (resid 90 through 190 )
12X-RAY DIFFRACTION12chain 'D' and (resid 3 through 55 )
13X-RAY DIFFRACTION13chain 'D' and (resid 56 through 76 )
14X-RAY DIFFRACTION14chain 'D' and (resid 77 through 101 )
15X-RAY DIFFRACTION15chain 'D' and (resid 102 through 154 )
16X-RAY DIFFRACTION16chain 'D' and (resid 155 through 181 )
17X-RAY DIFFRACTION17chain 'E' and (resid 2 through 32 )
18X-RAY DIFFRACTION18chain 'E' and (resid 33 through 89 )
19X-RAY DIFFRACTION19chain 'E' and (resid 90 through 133 )
20X-RAY DIFFRACTION20chain 'E' and (resid 134 through 162 )
21X-RAY DIFFRACTION21chain 'E' and (resid 163 through 190 )
22X-RAY DIFFRACTION22chain 'C' and (resid 1 through 13 )
23X-RAY DIFFRACTION23chain 'F' and (resid 1 through 13 )

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  • 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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