[English] 日本語
Yorodumi
- PDB-5whk: Crystal structure of Fab fragment of antibody DX-2507 bound to Fc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5whk
TitleCrystal structure of Fab fragment of antibody DX-2507 bound to FcRn-B2M
Components
  • Beta-2-microglobulin
  • DX-2507 Fab heavy chain
  • DX-2507 Fab light chain
  • IgG receptor FcRn large subunit p51
KeywordsIMMUNE SYSTEM / neonatal receptor / Fc / antibody recycling
Function / homology
Function and homology information


IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / immunoglobulin complex / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / immunoglobulin complex / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / endosome membrane / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain ...: / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IgG receptor FcRn large subunit p51 / Beta-2-microglobulin / IGL@ protein / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsEdwards, T.E. / Clifton, M.C. / Nixon, A.E. / Kenniston, J.A.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural basis for pH-insensitive inhibition of immunoglobulin G recycling by an anti-neonatal Fc receptor antibody.
Authors: Kenniston, J.A. / Taylor, B.M. / Conley, G.P. / Cosic, J. / Kopacz, K.J. / Lindberg, A.P. / Comeau, S.R. / Atkins, K. / Bullen, J. / TenHoor, C. / Adelman, B.A. / Sexton, D.J. / Edwards, T.E. / Nixon, A.E.
History
DepositionJul 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: DX-2507 Fab heavy chain
L: DX-2507 Fab light chain
A: IgG receptor FcRn large subunit p51
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7378
Polymers92,1984
Non-polymers5394
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-23 kcal/mol
Surface area34870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.560, 70.450, 256.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 2 molecules AB

#3: Protein IgG receptor FcRn large subunit p51 / FcRn / IgG Fc fragment receptor transporter alpha chain / Neonatal Fc receptor


Mass: 32824.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGRT, FCRN / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P55899
#4: Protein Beta-2-microglobulin


Mass: 13732.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P61769

-
Antibody , 2 types, 2 molecules HL

#1: Antibody DX-2507 Fab heavy chain


Mass: 22981.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: S6BAN1
#2: Antibody DX-2507 Fab light chain


Mass: 22659.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q6NS95

-
Non-polymers , 3 types, 258 molecules

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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: DX-2507 Fab FcRn B2M complex at 6.6 mg/mL at 70 uM against an optimization screen against JCSG+ A7 18% PEG 8000, 0.1 M CHES pH 9.8 with seeding from an earlier crystal obtained under similar ...Details: DX-2507 Fab FcRn B2M complex at 6.6 mg/mL at 70 uM against an optimization screen against JCSG+ A7 18% PEG 8000, 0.1 M CHES pH 9.8 with seeding from an earlier crystal obtained under similar conditions, supplemented with 20% ethylene glycol as cro-protectant

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→47.429 Å / Num. obs: 38312 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.888 % / Biso Wilson estimate: 44.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.081 / Χ2: 0.991 / Net I/σ(I): 16.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.564.980.6292.4227720.8150.703100
2.56-2.644.9990.5033.0527270.8970.561100
2.64-2.714.9810.3963.8226730.9320.443100
2.71-2.84.9830.2995.0425410.950.334100
2.8-2.894.9840.2516.1825070.9660.2899.9
2.89-2.994.980.1898.0124170.9760.211100
2.99-3.14.9530.159.9423390.9860.167100
3.1-3.234.9360.11912.2122390.990.133100
3.23-3.374.9360.09115.5821850.9940.102100
3.37-3.544.9060.07119.1320860.9960.07999.9
3.54-3.734.8770.06222.3619900.9960.0799.8
3.73-3.954.8860.05425.1218430.9970.06199.6
3.95-4.234.8260.04529.2217680.9970.0599.8
4.23-4.564.7940.03933.1716480.9980.04499.9
4.56-54.7460.03733.9415370.9980.04299.7
5-5.594.7770.03833.3413780.9980.04399.6
5.59-6.454.7140.0431.612610.9970.04699.8
6.45-7.914.6630.03234.4510580.9990.03799.5
7.91-11.184.4920.02740.048510.9980.03199.8
11.18-47.4293.9670.02440.34920.9990.02795

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX(1.10_2155)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M17, 5WHJ

3m17

5whj


Resolution: 2.5→47.429 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.37
RfactorNum. reflection% reflection
Rfree0.2246 1922 5.02 %
Rwork0.1693 --
obs0.1722 38303 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.05 Å2 / Biso mean: 49.4345 Å2 / Biso min: 20.32 Å2
Refinement stepCycle: final / Resolution: 2.5→47.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5830 0 34 254 6118
Biso mean--51.59 47.23 -
Num. residues----776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076029
X-RAY DIFFRACTIONf_angle_d0.9138223
X-RAY DIFFRACTIONf_chiral_restr0.048897
X-RAY DIFFRACTIONf_plane_restr0.0051060
X-RAY DIFFRACTIONf_dihedral_angle_d13.733536
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4999-2.56240.30791160.229425702686100
2.5624-2.63170.28131090.214325552664100
2.6317-2.70910.28331320.215926062738100
2.7091-2.79660.29211440.208425232667100
2.7966-2.89650.31531470.210925462693100
2.8965-3.01250.26141320.191125692701100
3.0125-3.14950.24231210.196926092730100
3.1495-3.31550.26711350.193325862721100
3.3155-3.52320.25691480.189325872735100
3.5232-3.79510.21971530.169325592712100
3.7951-4.17690.1751260.146526332759100
4.1769-4.78080.17391430.117126202763100
4.7808-6.02130.17111390.140226662805100
6.0213-47.43760.22171770.17022752292999
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)
11.4183-0.91640.24721.5608-0.07252.2051-0.1142-0.3990.79430.61390.17910.3504-1.1561-0.12650.01950.53480.26360.13060.46180.01090.398-15.22764.479846.5246
21.79260.3481-0.92792.2167-0.23243.93580.2905-0.58930.98760.43720.1607-0.109-1.22680.3638-0.31750.5385-0.01030.04870.3807-0.11240.3106-4.98717.652938.8704
32.681-0.8918-1.43332.4471-0.56253.93620.0781-0.00510.19780.15120.13820.1382-0.7652-0.3757-0.18650.32180.10080.04830.3385-0.04070.292-13.98762.421935.4154
42.4829-0.2959-2.75181.638-0.06143.097-0.31980.0664-0.07440.14520.26270.1933-0.2717-0.43990.04430.39640.15160.04680.4312-0.01790.4465-18.8894-1.192941.2958
51.7518-0.10510.1042.18930.55740.6227-0.0757-0.8041-0.61180.62330.1349-0.24990.31270.30960.01610.34220.08680.01760.4088-0.02150.3863-2.0835-3.091439.74
60.31390.4084-0.32220.60920.2352.40120.0925-0.03160.74980.3297-0.04320.6468-0.0506-0.7284-0.02820.44190.18710.21080.6405-0.04090.7119-25.82460.613853.5682
75.8904-0.45260.25152.60851.40245.02920.4551-0.5011-0.27580.3470.0584-0.1301-0.3059-0.4067-0.54210.4336-0.14820.20020.4282-0.04770.6046-18.3843-5.574574.1861
82.16440.45680.41862.240.4714.0620.3972-0.00320.51870.1892-0.1251-0.2719-0.23560.11-0.23810.4567-0.10640.26960.4764-0.09980.6472-14.3832-3.744268.4609
96.4169-0.89393.7385.5393-3.45874.10240.4443-0.70441.43880.6975-0.75560.0781-1.0420.1940.27120.6271-0.16140.23410.4865-0.16290.7926-16.82743.246174.7665
104.28221.57850.49712.107-0.51246.0099-0.2070.0165-0.631-0.25750.28120.25260.67810.37840.13460.47620.11430.09690.31310.060.5453-7.9904-24.611439.8407
111.66080.8149-0.94813.2662-1.41443.8529-0.251-0.1061-0.3144-0.116-0.0236-0.0670.47480.48150.11840.29660.11050.04830.3780.00940.3766-1.2305-15.988535.3965
120.40620.5523-0.99350.4704-0.51754.44540.0357-0.24860.00670.1664-0.30350.14840.50.31940.2560.4077-0.03390.14490.4204-0.03370.4292-13.7602-17.076358.945
132.14440.6199-0.45213.373-0.69843.97970.0339-0.18440.2093-0.1912-0.0013-0.03490.5416-0.2656-0.02250.5687-0.20170.21910.5-0.09920.4968-23.2-19.623373.0012
142.90260.17590.06083.1363-0.15473.0002-0.09930.2138-0.0376-0.76720.2082-0.29170.18750.1662-0.13270.3682-0.03660.06150.2959-0.01590.25418.382-1.76043.3293
151.99780.4479-1.3423.1117-0.80932.1535-0.0888-0.02690.1257-0.1315-0.0502-0.1804-0.04010.16550.09490.257-0.0032-0.00460.2874-0.02540.25539.73822.913613.359
163.39010.47745.0130.62931.59198.9956-0.00210.6160.3759-0.07540.4523-0.1867-0.41220.9159-0.08710.4611-0.14770.13960.43240.07220.439210.323913.8794-3.3803
174.001-1.06560.12852.7359-0.19953.5105-0.01980.1703-0.088-0.4798-0.06840.36020.4107-0.33470.14040.4866-0.0369-0.07830.2993-0.03150.3436-16.4685.4832-17.0141
181.3565-0.5452-0.30261.7088-0.67572.7921-0.05740.11260.1582-0.1265-0.20570.0577-0.7864-0.95760.19780.25850.00980.00430.2901-0.07040.3277-9.755-7.1212-1.8674
191.3067-0.3176-0.44681.50950.02264.3740.11840.330.1656-0.7361-0.080.0825-0.40230.56050.00430.65860.0356-0.00110.39390.0050.3105-4.5809-7.0133-15.7224
200.47190.97921.1052.86942.99293.3560.1367-0.1026-0.16050.4501-0.15940.01991.16390.00340.17180.48610.0479-0.01520.3504-0.07810.3916-4.6283-17.6123-6.0413
210.95781.37681.33131.64441.30478.5611-0.0215-0.049-0.1112-0.4819-0.1713-0.0697-0.43310.33160.08490.34680.0349-0.03620.3311-0.02540.327-1.383-9.0406-8.2294
222.27041.1162-0.48662.6590.99477.19640.01260.0490.0779-0.1292-0.0440.19650.6118-0.50480.0130.35070.0357-0.0830.3122-0.06270.3508-12.0654-14.488-7.897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 17 )H1 - 17
2X-RAY DIFFRACTION2chain 'H' and (resid 18 through 33 )H18 - 33
3X-RAY DIFFRACTION3chain 'H' and (resid 34 through 83 )H34 - 83
4X-RAY DIFFRACTION4chain 'H' and (resid 84 through 98 )H84 - 98
5X-RAY DIFFRACTION5chain 'H' and (resid 99 through 109 )H99 - 109
6X-RAY DIFFRACTION6chain 'H' and (resid 110 through 122 )H110 - 122
7X-RAY DIFFRACTION7chain 'H' and (resid 123 through 148 )H123 - 148
8X-RAY DIFFRACTION8chain 'H' and (resid 149 through 206 )H149 - 206
9X-RAY DIFFRACTION9chain 'H' and (resid 207 through 217 )H207 - 217
10X-RAY DIFFRACTION10chain 'L' and (resid 1 through 23 )L1 - 23
11X-RAY DIFFRACTION11chain 'L' and (resid 24 through 77 )L24 - 77
12X-RAY DIFFRACTION12chain 'L' and (resid 78 through 154 )L78 - 154
13X-RAY DIFFRACTION13chain 'L' and (resid 155 through 212 )L155 - 212
14X-RAY DIFFRACTION14chain 'A' and (resid 4 through 39 )A4 - 39
15X-RAY DIFFRACTION15chain 'A' and (resid 40 through 156 )A40 - 156
16X-RAY DIFFRACTION16chain 'A' and (resid 157 through 180 )A157 - 180
17X-RAY DIFFRACTION17chain 'A' and (resid 181 through 270 )A181 - 270
18X-RAY DIFFRACTION18chain 'B' and (resid 1 through 11 )B1 - 11
19X-RAY DIFFRACTION19chain 'B' and (resid 12 through 30 )B12 - 30
20X-RAY DIFFRACTION20chain 'B' and (resid 31 through 46 )B31 - 46
21X-RAY DIFFRACTION21chain 'B' and (resid 47 through 77 )B47 - 77
22X-RAY DIFFRACTION22chain 'B' and (resid 78 through 99 )B78 - 99

+
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