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- PDB-4gbx: Crystal structure of an immune complex at pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 4gbx
TitleCrystal structure of an immune complex at pH 6.5
Components
  • (HLA class II histocompatibility antigen, ...) x 4
  • synthetic peptidePeptide synthesis
KeywordsIMMUNE SYSTEM / immune complex / peptide loading / peptide editing / antigen presentation
Function / homology
Function and homology information


MHC class II protein complex assembly / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / 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 / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation ...MHC class II protein complex assembly / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / 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 / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / inflammatory response to antigenic stimulus / intermediate filament / transport vesicle membrane / T-helper 1 type immune response / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / negative regulation of inflammatory response to antigenic stimulus / negative regulation of T cell proliferation / positive regulation of T cell proliferation / MHC class II antigen presentation / detection of bacterium / T cell receptor binding / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / adaptive immune response / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / immune response / positive regulation of protein phosphorylation / lysosomal membrane / external side of plasma membrane / Golgi membrane / intracellular membrane-bounded organelle / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
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 ...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
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen, DM alpha chain / HLA class II histocompatibility antigen, DM beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsSethi, D.K. / Pos, W. / Wucherpfennig, K.W.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Crystal Structure of the HLA-DM-HLA-DR1 Complex Defines Mechanisms for Rapid Peptide Selection.
Authors: Pos, W. / Sethi, D.K. / Call, M.J. / Schulze, M.S. / Anders, A.K. / Pyrdol, J. / Wucherpfennig, K.W.
History
DepositionJul 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jul 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_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: HLA class II histocompatibility antigen, DM alpha chain
D: HLA class II histocompatibility antigen, DM beta chain
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
E: synthetic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8148
Polymers92,1515
Non-polymers6643
Water1,00956
1
C: HLA class II histocompatibility antigen, DM alpha chain
D: HLA class II histocompatibility antigen, DM beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4473
Polymers45,2262
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-33 kcal/mol
Surface area19280 Å2
MethodPISA
2
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
E: synthetic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3675
Polymers46,9253
Non-polymers4422
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-25 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.167, 126.032, 143.107
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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HLA class II histocompatibility antigen, ... , 4 types, 4 molecules CDAB

#1: Protein HLA class II histocompatibility antigen, DM alpha chain / MHC class II antigen DMA / Really interesting new gene 6 protein


Mass: 22992.891 Da / Num. of mol.: 1 / Mutation: D191N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: alpha chain, DMA, HLA-DM, HLA-DMA, MHC CLASS II MOLECULE, RING6
Plasmid: PEE14.1 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Lec3.2.8.1 / References: UniProt: P28067
#2: Protein HLA class II histocompatibility antigen, DM beta chain / MHC class II antigen DMB / Really interesting new gene 7 protein


Mass: 22233.170 Da / Num. of mol.: 1 / Mutation: S64C, D110N,
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: beta chain, DMB, HLA-DMB, MHC Class II molecule HLA-DM, RING7
Plasmid: pEE14.1 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Lec3.2.8.1 / References: UniProt: P28068
#3: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 22111.936 Da / Num. of mol.: 1 / Mutation: C90V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: alpha chain, HLA-DR1, HLA-DRA, HLA-DRA1, MHC Class II molecule
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01903
#4: Protein HLA class II histocompatibility antigen, DRB1-1 beta chain / MHC class II antigen DRB1*1 / DR-1 / DR1


Mass: 23735.449 Da / Num. of mol.: 1 / Mutation: S59C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: beta chain, HLA-DR1, HLA-DRB1, MHC Class II molecule / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04229, UniProt: P01911*PLUS

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Protein/peptide / Sugars / Non-polymers , 3 types, 60 molecules E

#5: Protein/peptide synthetic peptide / Peptide synthesis


Mass: 1077.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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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: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 6% PEG 20000, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. all: 27300 / Num. obs: 27191 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.5 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.9-33.70.875199.9
3-3.123.70.63199.8
3.12-3.273.70.368199.9
3.27-3.443.70.2161100
3.44-3.653.70.1341100
3.65-3.943.60.098199.9
3.94-4.333.60.0591100
4.33-4.963.60.049199.7
4.96-6.243.50.055199
6.24-403.40.029197.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1065refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→36.991 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 1.36 / Phase error: 26.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 1227 5 %
Rwork0.1979 --
obs0.2004 24550 99.57 %
all-27300 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.3169 Å2
Refinement stepCycle: LAST / Resolution: 3→36.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6088 0 42 56 6186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016323
X-RAY DIFFRACTIONf_angle_d1.2958612
X-RAY DIFFRACTIONf_dihedral_angle_d16.832269
X-RAY DIFFRACTIONf_chiral_restr0.087939
X-RAY DIFFRACTIONf_plane_restr0.0071120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.12010.35131410.31132517X-RAY DIFFRACTION100
3.1201-3.26210.28621460.26672563X-RAY DIFFRACTION100
3.2621-3.43390.28971280.22292562X-RAY DIFFRACTION100
3.4339-3.64890.29631060.20362594X-RAY DIFFRACTION100
3.6489-3.93030.27891370.21012578X-RAY DIFFRACTION100
3.9303-4.32530.22911290.17722593X-RAY DIFFRACTION100
4.3253-4.94990.1971370.14922609X-RAY DIFFRACTION100
4.9499-6.23150.23381430.19062616X-RAY DIFFRACTION99
6.2315-36.99360.25081600.2032691X-RAY DIFFRACTION98
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)
10.4725-0.2209-0.3280.5339-0.37220.8619-0.3064-0.24210.61890.64830.18790.5803-0.6608-0.1190.07841.21160.4933-0.13320.5822-0.1951.1091-57.358812.020813.284
20.3075-0.55950.52431.0192-0.98981.05740.00180.16670.10250.24480.26890.279-0.2337-0.1609-0.29831.33060.5559-0.0861.1434-0.39191.1682-65.105613.439817.8295
30.2073-0.6830.40442.4148-1.39750.80460.84270.15330.30610.94830.60940.0189-0.25740.288-0.62491.20460.3685-0.13841.025-0.24981.4391-65.201619.063824.1041
40.8457-0.47540.09681.37310.13560.4192-0.241-0.29360.73390.1909-0.06640.3924-0.5062-0.8202-0.01260.57960.3421-0.00940.6914-0.1340.8283-60.02251.394712.3894
53.41441.44191.19571.8614-0.6081.39950.1956-1.03950.122-0.1969-0.0565-0.1459-0.3135-0.59490.11670.71540.11560.28930.7623-0.26390.6381-67.1955-12.391624.9462
61.25241.23350.78851.9660.77491.0504-0.8988-0.65520.22880.62020.25570.1076-0.588-0.22410.17610.65010.33450.05270.7613-0.03810.7371-60.29482.204118.6938
71.06970.23251.08631.30330.04932.9484-0.083-0.88450.46080.231-0.02640.20590.3392-1.237-0.04170.46960.17330.13980.7771-0.1410.6018-59.3138-10.281727.7109
80.27230.1959-0.19030.1652-0.13240.1243-0.2651-0.17840.59880.5183-0.0031-0.6361-0.32580.06240.14541.26950.2829-0.2910.6486-0.19161.0294-54.37112.92368.3687
9-0.0020.0723-0.04390.4145-0.30010.2154-0.3596-0.16521.03520.3039-0.3223-0.2263-0.9072-0.10070.45231.96970.0252-0.4970.2154-0.21331.2188-49.433420.395510.6683
103.49642.15290.07611.3276-0.01291.3990.10350.31680.27120.14080.16840.1451-1.4216-0.2006-0.03811.2550.137-0.02560.60310.08390.8826-50.305612.52280.2704
111.17921.370.28961.72750.84031.84710.0090.68970.50310.13070.2321-0.7991-0.2887-0.1896-0.56761.6598-0.0686-0.16230.86740.34031.3601-50.389116.7006-6.4171
120.0777-0.02430.03410.0064-0.00740.0125-0.2534-0.06230.90831.17730.1043-0.2525-0.01260.11770.41151.72510.31250.11470.6481-0.01021.6807-55.098126.36212.8083
130.35070.3109-0.71791.0186-0.4261.5522-0.213-0.49820.43470.6664-0.10780.4134-0.48180.03150.37610.81630.2248-0.12520.7798-0.38360.7087-43.2496-4.758239.1748
140.9142-0.69280.61341.0021-0.39070.94530.02640.04810.4191-0.2956-0.0162-0.0983-0.38820.552-0.06111.001-0.0418-0.13460.7272-0.28490.8485-37.97241.750538.4501
151.20291.35020.1244.3848-0.45073.9058-0.6581-0.37440.4666-0.15460.21160.5171-0.06380.4861-0.0070.76420.17150.19530.5219-0.45290.8625-49.41723.302728.311
163.44190.14640.87291.81621.25252.2543-0.3802-0.53050.1350.7585-0.0196-0.1319-0.47440.3269-0.29491.16210.2788-0.10170.7797-0.54110.521-36.2669-6.080645.1304
171.4239-0.86530.83631.6215-0.31561.4604-0.2831-0.57980.67190.57040.0112-0.00470.01210.0782-0.17751.39660.4061-0.18970.931-0.71020.8619-41.61713.995945.934
180.21820.3184-0.62291.9953-0.12852.0287-0.17160.27240.4560.02450.07860.0578-0.1329-0.23940.12780.29480.0206-0.0330.31990.03520.4582-46.2275-13.1716-1.6973
190.5846-0.29141.17780.1616-0.64652.6534-0.3106-0.07530.9729-0.5635-0.19970.2486-0.8805-0.10210.22450.8852-0.19-0.18750.1910.00831.2346-45.9742-1.27853.6464
201.7120.0209-0.79691.16190.27421.7948-0.07080.14110.3090.03440.06840.06670.0601-0.09370.01440.21230.0099-0.04560.39510.03760.3028-49.7612-23.95343.0823
211.9140.2316-1.02851.71591.97736.53550.1351-0.1906-0.25860.37730.0375-0.07580.8634-0.6821-0.1210.3875-0.11140.04570.46710.04670.3856-54.905-33.290513.5626
222.62491.42221.84872.05191.84962.19650.03560.23690.17720.187-0.02570.023-0.06160.23-0.00070.2816-0.04310.02750.3870.03190.3361-40.7443-20.3999-8.458
231.6752-0.6405-0.21690.27450.0722.9536-0.02170.36740.3858-0.0847-0.0354-0.2038-0.37990.24690.06390.3345-0.1337-0.00290.39670.06120.4444-33.3798-14.4841-2.334
242.35820.26530.02571.13241.04982.3923-0.1694-0.2569-0.00440.6530.1783-0.11590.33220.6716-0.02850.44580.1141-0.03710.4369-0.07250.3847-30.1004-24.368926.4315
252.3628-0.60230.02681.1996-1.38531.8222-0.40750.1375-0.12050.2034-0.1106-0.2699-0.4061-0.1190.58980.378-0.1606-0.06890.77890.08150.7923-41.1958-9.1352-16.2979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 12 through 37 )
2X-RAY DIFFRACTION2chain 'C' and (resid 38 through 54 )
3X-RAY DIFFRACTION3chain 'C' and (resid 55 through 69 )
4X-RAY DIFFRACTION4chain 'C' and (resid 70 through 130 )
5X-RAY DIFFRACTION5chain 'C' and (resid 131 through 142 )
6X-RAY DIFFRACTION6chain 'C' and (resid 143 through 162 )
7X-RAY DIFFRACTION7chain 'C' and (resid 163 through 202 )
8X-RAY DIFFRACTION8chain 'D' and (resid 3 through 14 )
9X-RAY DIFFRACTION9chain 'D' and (resid 15 through 28 )
10X-RAY DIFFRACTION10chain 'D' and (resid 29 through 38 )
11X-RAY DIFFRACTION11chain 'D' and (resid 39 through 65 )
12X-RAY DIFFRACTION12chain 'D' and (resid 66 through 91 )
13X-RAY DIFFRACTION13chain 'D' and (resid 92 through 119 )
14X-RAY DIFFRACTION14chain 'D' and (resid 120 through 143 )
15X-RAY DIFFRACTION15chain 'D' and (resid 144 through 157 )
16X-RAY DIFFRACTION16chain 'D' and (resid 158 through 177 )
17X-RAY DIFFRACTION17chain 'D' and (resid 178 through 193 )
18X-RAY DIFFRACTION18chain 'A' and (resid 3 through 45 )
19X-RAY DIFFRACTION19chain 'A' and (resid 46 through 58 )
20X-RAY DIFFRACTION20chain 'A' and (resid 59 through 154 )
21X-RAY DIFFRACTION21chain 'A' and (resid 155 through 182 )
22X-RAY DIFFRACTION22chain 'B' and (resid -5 through 32 )
23X-RAY DIFFRACTION23chain 'B' and (resid 33 through 122 )
24X-RAY DIFFRACTION24chain 'B' and (resid 123 through 190 )
25X-RAY DIFFRACTION25chain 'E' and (resid 84 through 93 )

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  • 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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