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- PDB-7uvf: Crystal structure of ZED8 Fab complex with CD8 alpha -

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Basic information

Entry
Database: PDB / ID: 7uvf
TitleCrystal structure of ZED8 Fab complex with CD8 alpha
Components
  • (Immunoglobulin ...) x 2
  • T-cell surface glycoprotein CD8 alpha chain
KeywordsIMMUNE SYSTEM / imaging / cd8
Function / homology
Function and homology information


cytotoxic T cell differentiation / MHC class I protein complex binding / T cell mediated immunity / T cell receptor complex / MHC class I protein binding / plasma membrane raft / antigen processing and presentation / coreceptor activity / cell surface receptor protein tyrosine kinase signaling pathway / T cell activation ...cytotoxic T cell differentiation / MHC class I protein complex binding / T cell mediated immunity / T cell receptor complex / MHC class I protein binding / plasma membrane raft / antigen processing and presentation / coreceptor activity / cell surface receptor protein tyrosine kinase signaling pathway / T cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor signaling pathway / adaptive immune response / cell surface receptor signaling pathway / receptor complex / immune response / external side of plasma membrane / extracellular region / plasma membrane
Similarity search - Function
CD8 alpha subunit / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T-cell surface glycoprotein CD8 alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYu, C. / Davies, C. / Koerber, J.T. / Williams, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Eur J Nucl Med Mol Imaging / Year: 2023
Title: Preclinical development of ZED8, an 89 Zr immuno-PET reagent for monitoring tumor CD8 status in patients undergoing cancer immunotherapy.
Authors: Ogasawara, A. / Kiefer, J.R. / Gill, H. / Chiang, E. / Sriraman, S. / Ferl, G.Z. / Ziai, J. / Bohorquez, S.S. / Guelman, S. / Wang, X. / Yang, J. / Phan, M.M. / Nguyen, V. / Chung, S. / Yu, ...Authors: Ogasawara, A. / Kiefer, J.R. / Gill, H. / Chiang, E. / Sriraman, S. / Ferl, G.Z. / Ziai, J. / Bohorquez, S.S. / Guelman, S. / Wang, X. / Yang, J. / Phan, M.M. / Nguyen, V. / Chung, S. / Yu, C. / Tinianow, J. / Waaijer, S.J.H. / De Crespigny, A. / Marik, J. / Boswell, C.A. / Zabka, T. / Staflin, K. / Williams, S.P.
History
DepositionMay 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 18, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-cell surface glycoprotein CD8 alpha chain
B: T-cell surface glycoprotein CD8 alpha chain
H: Immunoglobulin heavy chain
L: Immunoglobulin light chain
Y: Immunoglobulin light chain
X: Immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,8389
Polymers122,6756
Non-polymers1633
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)268.968, 59.441, 111.377
Angle α, β, γ (deg.)90.000, 112.290, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein T-cell surface glycoprotein CD8 alpha chain / T-lymphocyte differentiation antigen T8/Leu-2


Mass: 14425.239 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD8A, MAL / Production host: Escherichia coli (E. coli) / References: UniProt: P01732

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Antibody , 2 types, 4 molecules HXLY

#2: Antibody Immunoglobulin heavy chain


Mass: 23474.221 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)
#3: Antibody Immunoglobulin light chain


Mass: 23437.936 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)

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Non-polymers , 3 types, 175 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.36 Å3/Da / Density % sol: 63.37 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 6
Details: 0.1M ammonium acetate 0.1M Bis-Tris pH6.0 17% PEG 10K

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 48140 / % possible obs: 94.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.05 / Rrim(I) all: 0.089 / Χ2: 1.002 / Net I/σ(I): 8.4 / Num. measured all: 151360
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.6-2.641.90.83819470.4420.6750.85478.4
2.64-2.692.20.83121890.3990.6340.92585.9
2.69-2.742.40.78222900.5050.5750.92791.90.977
2.74-2.82.60.62922660.5850.4560.94190.20.781
2.8-2.8630.58923430.7140.40.9592.50.716
2.86-2.933.30.45124600.790.2870.97598.50.537
2.93-33.40.36625140.8460.2310.94198.20.435
3-3.083.40.29924780.8890.1910.94998.70.357
3.08-3.173.40.23324800.940.1480.958980.277
3.17-3.283.30.19524580.9550.1260.99297.30.233
3.28-3.393.20.15124430.9730.0991.0197.30.181
3.39-3.533.30.10723010.9840.071.05290.30.128
3.53-3.693.50.09924890.9860.0621.24498.30.117
3.69-3.883.40.07824750.9920.0491.05698.10.092
3.88-4.133.40.05825180.9960.0370.99198.60.069
4.13-4.443.30.04525080.9970.0291.0298.20.054
4.44-4.893.40.03724040.9980.0241.03393.50.044
4.89-5.63.50.03625340.9980.0220.9599.30.043
5.6-7.053.20.03724560.9970.0240.98994.80.045
7.05-403.40.02625870.9990.0171.05496.70.032

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX1.16refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Internal

Resolution: 2.6→34.3545 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 2430 5.05 %
Rwork0.1978 45698 -
obs0.2008 48128 94.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.14 Å2 / Biso mean: 76.7955 Å2 / Biso min: 30.39 Å2
Refinement stepCycle: final / Resolution: 2.6→34.3545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8170 0 8 172 8350
Biso mean--63.99 53.29 -
Num. residues----1078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088394
X-RAY DIFFRACTIONf_angle_d1.01411450
X-RAY DIFFRACTIONf_dihedral_angle_d6.2755389
X-RAY DIFFRACTIONf_chiral_restr0.0561300
X-RAY DIFFRACTIONf_plane_restr0.0071479
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.64940.38621100.3539217577
2.6494-2.7070.37311290.3206245187
2.707-2.770.33971390.2894260894
2.77-2.83920.31541410.2649251989
2.8392-2.91590.30861610.2552273999
2.9159-3.00170.30421570.2567279098
3.0017-3.09850.32581400.2497277098
3.0985-3.20920.30231450.2335274898
3.2092-3.33760.3421470.2353277497
3.3376-3.48930.26711250.2182259791
3.4893-3.67310.34011360.2153275898
3.6731-3.90290.26031700.1952278598
3.9029-4.20380.23681460.1691280999
4.2038-4.62590.18851260.1457268994
4.6259-5.29320.20171530.1414285599
5.2932-6.66090.23381470.1793280297
6.6609-34.35450.20731580.1778282995
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.52910.16040.73582.49431.32230.93620.10060.27780.03450.0615-0.36430.2077-0.33050.12210.00050.5004-0.0020.03640.3603-0.02890.3991-72.30835.63551.66
21.7958-0.39920.13352.4345-0.96891.62020.05610.26170.01060.0059-0.0622-0.4062-0.34260.2358-0.00030.51390.00760.03770.3806-0.0660.4469-67.1136.9251.359
33.0990.20771.84842.328-0.23161.20130.21780.60680.3711-0.37450.0214-0.5499-0.4090.1993-0.00010.6252-0.06450.10330.3803-0.01430.5461-69.91161.42759.618
43.2441-0.7561.24222.88862.10252.6695-0.040.52650.1435-0.25390.22590.3913-0.3651-0.54870.00090.7017-0.02590.040.40090.0480.5241-79.0556.88253.06
53.3475-0.87930.91751.97171.20351.43330.07510.1341-0.0456-0.4538-0.0245-0.2206-0.2787-0.09170.00030.5793-0.0540.06350.24750.01410.4413-74.22355.79261.02
60.83450.31090.42741.2176-0.740.948-0.2848-0.6307-0.5202-0.04330.12040.1540.32950.3868-0.01370.64120.074-0.05380.5330.02080.6818-55.2514.17780.002
71.23860.1970.49343.9757-0.4343.0208-0.13270.0015-0.32420.0702-0.1176-0.35140.00720.2863-0.00010.41220.012-0.00250.3402-0.00010.463-60.47812.98772.609
80.97630.04730.80321.0760.36480.7572-0.28140.2417-0.3580.08830.2179-0.06360.6387-0.03230.00030.51080.05480.04460.52-0.02330.5643-63.0565.74471.791
90.39060.32050.1890.8567-0.40130.6090.73960.1277-0.2921-0.9283-0.4791-0.5903-0.58410.3462-0.00070.5090.0693-0.02260.52220.07620.7334-51.0058.28173.214
100.98980.76920.50870.62110.32762.4365-0.0655-0.3145-0.13160.4522-0.2726-0.48370.03050.4598-0.00060.4892-0.01820.03030.55720.10270.6789-52.94710.57578.439
110.0031-0.04320.04440.2859-0.28030.273-0.5156-0.2639-0.91350.45630.39230.1148-0.69740.6035-0.00030.91340.1184-0.16961.25050.11640.9814-27.5830.12894.914
120.6150.04870.05942.0297-0.36450.1293-0.0037-0.3078-0.04770.5643-1.0174-0.186-0.11470.808900.7408-0.1382-0.14551.37170.20420.9692-32.993.75496.504
130.0996-0.0645-0.130.08190.16370.2806-0.0919-0.44920.11380.4828-0.43650.16610.25030.3572-0.00270.8574-0.0911-0.10081.13380.14550.9336-34.912-4.83198.394
142.0568-0.58881.94561.854-1.17432.4134-0.2463-0.30.48020.6027-0.2847-0.627-0.68170.3441-0.00150.7227-0.1617-0.21180.576-0.01910.7822-49.6830.0679.082
150.1910.1995-0.1550.2776-0.30810.4318-0.479-1.02860.38860.5445-0.446-0.8471-0.48470.1842-0.20630.9402-0.3793-0.57171.29110.34241.0537-31.71524.79492.839
162.08311.35350.31651.6141-0.59441.1602-0.13950.4832-0.06060.2303-0.3017-0.7047-0.10611.00720.00020.7159-0.0411-0.13991.60990.381.1976-23.2548.63988.931
170.1192-0.4409-0.13341.71090.48410.1846-0.13880.24720.3027-0.4730.1613-1.2867-0.34950.76280.0250.6558-0.1152-0.18631.50330.40751.8659-13.64612.39390.495
180.3614-0.46010.32950.93460.01720.84440.2181-0.3065-1.17840.3183-0.28390.2295-0.1208-0.5582-0.02970.598-0.21950.02840.67980.18160.8908-109.05846.4275.075
190.77230.4005-0.02720.673-0.34910.51570.1479-0.7146-0.811-0.2182-0.07080.20610.1777-0.30160.00150.6314-0.108-0.00070.5260.15640.5642-99.76649.22172.209
200.3187-0.10910.11530.60870.44850.4527-0.1169-1.3382-1.1155-0.4569-0.31420.04140.21250.0714-0.12970.7751-0.0720.18920.99110.51240.8617-96.72943.58783.456
210.37-0.08940.31670.66810.14750.3517-0.2605-0.65-1.24870.07490.27760.4340.752-0.51270.03380.7745-0.1730.04280.7270.370.925-102.89143.19877.352
220.1014-0.00070.17570.2899-0.01940.317-0.23740.15280.1115-0.3550.49920.43380.4971-0.76990.00060.5274-0.059-0.0120.54440.0750.4464-97.88257.41673.868
231.75990.3794-0.30020.6425-0.37310.21990.032-0.6613-0.01280.0420.01580.51220.2634-0.31280.16250.6447-0.45170.07091.16580.6231.2205-122.64142.55684.834
241.78170.71040.38581.1432-0.40831.5859-0.4269-0.90160.1924-0.19440.05970.5032-0.0575-0.5113-0.25610.6365-0.2579-0.02931.79130.6220.9419-133.19659.45691.379
250.21520.49880.56581.17671.33071.5165-0.1356-0.23590.2951-0.9264-0.31580.30590.2596-0.9802-0.14750.6754-0.182-0.1051.49560.49510.8479-133.40264.42383.857
260.22720.2543-0.40720.2874-0.50241.3623-0.4865-0.3701-0.35650.22350.02730.23210.91130.24960.13160.7407-0.24970.13431.37540.85691.1102-120.7945.77991.02
270.0420.00870.0130.292-0.09730.3008-0.1815-0.13090.6543-0.2645-0.18020.494-0.00320.15270.0050.4488-0.0497-0.13851.60760.35121.1952-137.10669.20990.509
280.1573-0.09090.01640.2888-0.27430.2950.01030.33090.2123-0.14960.07610.15480.1282-0.558-0.00110.5606-0.0984-0.12041.58940.39371.2653-140.5755.60887.139
291.2573-0.8579-0.06841.3772-0.1580.89180.241-1.1503-0.0815-0.59220.02270.0647-0.05730.16090.12560.59150.07560.27051.4558-0.18340.3643-98.92164.91295.231
302.65090.5667-0.9410.1773-0.13670.46240.0884-1.7073-0.20710.5731-0.0978-0.25980.30680.21350.16890.5831-0.1108-0.03681.5371-0.02110.2602-89.97661.3490.248
310.13660.1832-0.36161.3094-0.45650.95250.2003-1.13830.6508-0.0838-0.24670.45410.0149-0.3985-0.00050.4726-0.1028-0.04110.7681-0.09030.4746-97.25862.8781.618
320.7790.6830.00441.20040.66780.71720.118-1.37820.43480.0880.0654-0.259-0.35160.17590.01070.5554-0.05980.03911.1139-0.18550.4475-88.65768.85686.692
331.86790.9457-0.32510.74460.36941.23030.0663-1.5639-0.09210.07640.02270.1539-0.0204-0.12620.00120.529-0.06330.00970.98690.07920.4287-96.35360.76185.635
342.608-0.7755-1.43120.63280.3360.794-0.7507-1.1270.64660.42010.3080.21570.2977-0.9824-0.20060.487-0.00190.24111.5197-0.22340.5136-111.4272.50195.737
350.44180.2702-0.45110.71560.08130.7852-0.5509-1.0991-0.0243-0.94710.46910.55020.12420.2052-0.04780.60740.029-0.02161.97170.3340.7776-130.59261.014101.074
360.8663-0.1996-0.18221.64220.06960.9137-0.1442-1.6067-0.59120.19830.55770.3760.1882-0.1499-0.08190.3444-0.08110.25162.33860.77540.7691-124.11557.589101.828
375.13931.9602-2.07771.3688-0.24811.341-0.1078-1.34390.12350.62510.46050.66570.1660.03280.95210.37110.07490.27852.2050.08210.8758-122.52264.668108.657
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:46 )A1 - 46
2X-RAY DIFFRACTION2( CHAIN A AND RESID 47:117 )A47 - 117
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1:32 )B1 - 32
4X-RAY DIFFRACTION4( CHAIN B AND RESID 33:73 )B33 - 73
5X-RAY DIFFRACTION5( CHAIN B AND RESID 74:117 )B74 - 117
6X-RAY DIFFRACTION6( CHAIN H AND RESID 1:17 )H1 - 17
7X-RAY DIFFRACTION7( CHAIN H AND RESID 18:63 )H18 - 63
8X-RAY DIFFRACTION8( CHAIN H AND RESID 64:82 )H64 - 82
9X-RAY DIFFRACTION9( CHAIN H AND RESID 83:95 )H83 - 95
10X-RAY DIFFRACTION10( CHAIN H AND RESID 97:119 )H97 - 119
11X-RAY DIFFRACTION11( CHAIN H AND RESID 120:145 )H120 - 145
12X-RAY DIFFRACTION12( CHAIN H AND RESID 146:193 )H146 - 193
13X-RAY DIFFRACTION13( CHAIN H AND RESID 194:213 )H194 - 213
14X-RAY DIFFRACTION14( CHAIN L AND RESID 1:101 )L1 - 101
15X-RAY DIFFRACTION15( CHAIN L AND RESID 102:115 )L102 - 115
16X-RAY DIFFRACTION16( CHAIN L AND RESID 116:187 )L116 - 187
17X-RAY DIFFRACTION17( CHAIN L AND RESID 188:211 )L188 - 211
18X-RAY DIFFRACTION18( CHAIN Y AND RESID 1:18 )Y1 - 18
19X-RAY DIFFRACTION19( CHAIN Y AND RESID 19:38 )Y19 - 38
20X-RAY DIFFRACTION20( CHAIN Y AND RESID 39:61 )Y39 - 61
21X-RAY DIFFRACTION21( CHAIN Y AND RESID 62:90 )Y62 - 90
22X-RAY DIFFRACTION22( CHAIN Y AND RESID 91:102 )Y91 - 102
23X-RAY DIFFRACTION23( CHAIN Y AND RESID 103:114 )Y103 - 114
24X-RAY DIFFRACTION24( CHAIN Y AND RESID 115:150 )Y115 - 150
25X-RAY DIFFRACTION25( CHAIN Y AND RESID 151:163 )Y151 - 163
26X-RAY DIFFRACTION26( CHAIN Y AND RESID 164:174 )Y164 - 174
27X-RAY DIFFRACTION27( CHAIN Y AND RESID 175:190 )Y175 - 190
28X-RAY DIFFRACTION28( CHAIN Y AND RESID 191:213 )Y191 - 213
29X-RAY DIFFRACTION29( CHAIN X AND RESID 1:16 )X1 - 16
30X-RAY DIFFRACTION30( CHAIN X AND RESID 17:39 )X17 - 39
31X-RAY DIFFRACTION31( CHAIN X AND RESID 40:52 )X40 - 52
32X-RAY DIFFRACTION32( CHAIN X AND RESID 53:82 )X53 - 82
33X-RAY DIFFRACTION33( CHAIN X AND RESID 83:106 )X83 - 106
34X-RAY DIFFRACTION34( CHAIN X AND RESID 107:118 )X107 - 118
35X-RAY DIFFRACTION35( CHAIN X AND RESID 120:145 )X120 - 145
36X-RAY DIFFRACTION36( CHAIN X AND RESID 146:199 )X146 - 199
37X-RAY DIFFRACTION37( CHAIN X AND RESID 200:213 )X200 - 213

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Feb 9, 2022. New format data for meta-information of EMDB entries

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  • Version 3 of the EMDB header file is now the official format.
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