[English] 日本語
Yorodumi
- PDB-6cxy: Crystal Structure of Human E-cadherin bound by mouse monoclonal a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cxy
TitleCrystal Structure of Human E-cadherin bound by mouse monoclonal antibody Fab mAb-1_19A11
Components
  • Cadherin-1
  • Heavy chain
  • Light Chain
KeywordsCELL ADHESION / SSGCID / Cadherin-1 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


response to heparin / desmosome assembly / response to Gram-positive bacterium / pituitary gland development / gamma-catenin binding / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of axon extension / desmosome / cellular response to indole-3-methanol / calcium-dependent cell-cell adhesion ...response to heparin / desmosome assembly / response to Gram-positive bacterium / pituitary gland development / gamma-catenin binding / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of axon extension / desmosome / cellular response to indole-3-methanol / calcium-dependent cell-cell adhesion / flotillin complex / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / cell-cell adhesion mediated by cadherin / adherens junction organization / Formation of definitive endoderm / catenin complex / Apoptotic cleavage of cell adhesion proteins / cell-cell junction assembly / Adherens junctions interactions / GTPase activating protein binding / ankyrin binding / negative regulation of cell-cell adhesion / cellular response to lithium ion / apical junction complex / homophilic cell-cell adhesion / lateral plasma membrane / Integrin cell surface interactions / RHO GTPases activate IQGAPs / synapse assembly / cell adhesion molecule binding / positive regulation of protein localization / Degradation of the extracellular matrix / Transcriptional and post-translational regulation of MITF-M expression and activity / InlA-mediated entry of Listeria monocytogenes into host cells / protein tyrosine kinase binding / negative regulation of cell migration / protein localization to plasma membrane / adherens junction / trans-Golgi network / cell-cell adhesion / beta-catenin binding / positive regulation of protein import into nucleus / response to toxic substance / cytoplasmic side of plasma membrane / cell morphogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / neuron projection development / cell junction / cell migration / lamellipodium / actin cytoskeleton / regulation of gene expression / postsynapse / endosome / cadherin binding / response to xenobiotic stimulus / calcium ion binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / glutamatergic synapse / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Cadherins / Cadherin conserved site / Cadherin domain signature. ...Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody Fab mAb-1_19A11
Authors: Dranow, D.M. / Phan, J.N. / Maker, A.Y. / Schecterson, L.C. / Mangio, R.S. / Gumbiner, B.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionApr 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Cadherin-1
H: Heavy chain
L: Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,73225
Polymers72,3003
Non-polymers1,43222
Water11,494638
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint10 kcal/mol
Surface area29910 Å2
Unit cell
Length a, b, c (Å)122.680, 77.470, 110.940
Angle α, β, γ (deg.)90.000, 92.910, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-694-

HOH

21C-751-

HOH

31H-457-

HOH

41H-571-

HOH

-
Components

-
Protein , 1 types, 1 molecules C

#1: Protein Cadherin-1 / CAM 120/80 / Epithelial cadherin / E-cadherin / Uvomorulin


Mass: 23595.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH1, CDHE, UVO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12830

-
Antibody , 2 types, 2 molecules HL

#2: Antibody Heavy chain


Mass: 24385.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ighg1 / Plasmid: pcDNA3.4 / Cell line (production host): Expi-293F / Production host: Homo sapiens (human)
#3: Antibody Light Chain


Mass: 24319.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: LC / Plasmid: pcDNA3.4 / Cell line (production host): Expi293F / Production host: Homo sapiens (human)

-
Non-polymers , 4 types, 660 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / 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: 3.64 Å3/Da / Density % sol: 66.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: HosaA.19747.a.KW2.PC00156 at 10.3 mg/ml in a buffer containing 50 mM Tris, pH = 8, 150 mM NaCl, and 3 mM CaCl2 was mixed 0.1 uL + 0.1 uL with Wizard 3/4 (h12): 15% (w/v) PEG-20,000, 0.1 M ...Details: HosaA.19747.a.KW2.PC00156 at 10.3 mg/ml in a buffer containing 50 mM Tris, pH = 8, 150 mM NaCl, and 3 mM CaCl2 was mixed 0.1 uL + 0.1 uL with Wizard 3/4 (h12): 15% (w/v) PEG-20,000, 0.1 M HEPES/ NaOH, pH = 7.0. The crystal was cryoprotected with 20% ethylene glycol. Tray: 299140h12, puck: qxp2-3

-
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: Mar 22, 2018 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→40.091 Å / Num. obs: 52838 / % possible obs: 99.9 % / Redundancy: 4.19 % / Biso Wilson estimate: 31.67 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.094 / Χ2: 1.03 / Net I/σ(I): 13.4 / Num. measured all: 221388 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.264.2460.5872.616425387138680.7840.67299.9
2.26-2.324.2530.5113.0216093378637840.830.58499.9
2.32-2.394.2470.4193.6115557366536630.8690.4899.9
2.39-2.464.2540.3714.1115307360035980.8910.42499.9
2.46-2.544.2510.3114.8914722346034630.9230.356100
2.54-2.634.2620.2516.0314334336933630.9510.28799.8
2.63-2.734.2550.1997.5113812324732460.9690.227100
2.73-2.844.2340.169.2413282313931370.9780.18399.9
2.84-2.974.230.12211.8612602298029790.9870.14100
2.97-3.114.1980.10113.9212112288628850.990.116100
3.11-3.284.1670.07917.2911530276827670.9940.091100
3.28-3.484.1140.06420.5210594257525750.9960.073100
3.48-3.724.0750.05224.349817241124090.9970.0699.9
3.72-4.024.0550.04726.249237227822780.9970.054100
4.02-4.44.0460.0429.258367207020680.9980.04699.9
4.4-4.924.0930.03531.457772190018990.9980.0499.9
4.92-5.684.110.03530.826941169116890.9990.0499.9
5.68-6.964.140.036295937143514340.9990.04199.9
6.96-9.844.1070.02932.924542110711060.9990.03399.9
9.84-40.0913.8360.02536.4424056406270.9990.02998

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.2 Å40.09 Å
Translation2.2 Å40.09 Å

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2o72, 4web

2o72

4web


Resolution: 2.2→40.091 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2648 5.01 %Random selection
Rwork0.1626 50185 --
obs0.1644 52833 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.39 Å2 / Biso mean: 36.399 Å2 / Biso min: 7.31 Å2
Refinement stepCycle: final / Resolution: 2.2→40.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4849 0 90 646 5585
Biso mean--58.25 43.61 -
Num. residues----640
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1999-2.23990.31021430.23725862729
2.2399-2.28290.27031250.222526632788
2.2829-2.32950.2781230.202926312754
2.3295-2.38020.23581310.198126242755
2.3802-2.43550.26781400.191926222762
2.4355-2.49640.26541420.196626532795
2.4964-2.56390.23111130.196326272740
2.5639-2.63940.23621320.180626392771
2.6394-2.72450.22551330.179326292762
2.7245-2.82190.23471440.178526352779
2.8219-2.93480.24281310.174626592790
2.9348-3.06840.22371680.19126152783
3.0684-3.23010.24561640.180526222786
3.2301-3.43230.24081330.176526432776
3.4323-3.69720.1791300.16126452775
3.6972-4.06890.17911270.148126882815
4.0689-4.65690.13671920.113425892781
4.6569-5.86430.1221410.113626812822
5.8643-40.09780.14661360.143927342870
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)
10.39410.17110.31071.27221.38862.4864-0.02160.0661-0.03270.11460.0375-0.0085-0.0355-0.025-0.03150.24780.0111-0.00650.2410.02870.2026-3.0961-3.502348.9508
24.0863-1.2354-1.3413.39830.78165.83660.09340.33880.0209-0.0481-0.0510.1989-0.1698-0.4139-0.03350.16770.0021-0.05020.2112-0.00370.1595-8.29760.901941.7784
33.4358-3.2011-0.79635.28110.9871.9416-0.0558-0.00330.28990.01680.1201-0.3877-0.03470.0516-0.06860.2067-0.0013-0.02240.23770.01410.1787-0.811.884942.4139
49.5065-2.5263-6.07791.73091.19385.1957-0.00510.6061-0.28160.0173-0.17650.19270.082-0.46020.14680.27350.0329-0.06530.3097-0.01740.292120.6598-18.481533.9689
57.4775-2.8438-0.53422.19550.1870.5620.04890.1196-0.0637-0.1142-0.04680.02350.17480.0815-0.00860.26330.0378-0.02650.22620.01780.18636.5926-25.469634.6459
62.3514-2.75131.1765.01730.34962.24860.3061.3445-0.0551-0.3686-0.321-0.35630.23990.1243-0.04790.33390.1146-0.04720.3784-0.00120.170638.5341-25.916226.7251
73.1958-2.4217-2.7732.59373.40964.90450.025-0.06640.5929-0.66630.2466-0.8649-0.22810.3973-0.12570.3146-0.0036-0.02230.3184-0.06990.3839-1.883-27.572815.5321
82.062-0.16240.18734.20971.87452.0049-0.01510.169-0.0483-0.05440.107-0.2985-0.08120.2019-0.09540.3024-0.02190.02150.295-0.040.2728-1.7167-22.537226.6253
92.8436-1.0593-0.27036.4823.11414.20180.02310.1548-0.0476-0.11430.0854-0.3325-0.18350.3243-0.08510.2619-0.00810.0080.3323-0.01740.2183-0.3964-27.126621.0304
101.2361-0.4345-0.55025.87245.26115.27750.0221-0.1122-0.06610.1575-0.17720.0935-0.3091-0.18030.21870.27380.0249-0.03940.2669-0.00950.2015-12.0697-16.632630.7305
110.58321.20930.08744.90913.90365.879-0.04290.09060.04790.10240.0935-0.10610.01380.1036-0.02260.23980.03740.02040.2372-0.02380.2994-3.3183-36.906210.3484
128.0177-4.1823-3.00585.90571.42064.6970.23491.0633-0.7668-0.4394-0.08390.2465-0.0626-0.3612-0.1570.3651-0.0195-0.02780.2420.05490.2455-22.3915-42.6426-1.1119
134.3104-3.97233.68474.8631-1.9895.2329-0.0469-0.3930.8767-0.09980.1587-0.3303-0.167-0.0886-0.10910.3467-0.0020.02120.24140.00480.3123-15.4246-34.69254.5985
145.5811-0.12373.15593.1941-1.76426.31430.1678-0.0295-0.3199-0.1262-0.00130.20480.05780.1124-0.13660.2723-0.04290.02620.2023-0.00350.2345-19.7891-41.10516.4183
152.4537-2.46672.32463.7083-0.80294.27740.18540.78620.4616-0.5293-0.11620.20750.14210.00760.0160.473-0.0185-0.01050.34210.06460.3575-19.665-35.335-4.4487
164.53882.50692.87832.79940.61973.59120.45-0.2261-0.19150.6199-0.40810.13360.6889-0.30860.03530.4486-0.07980.12450.3383-0.04580.3453-22.059-35.695737.626
172.99681.45141.28093.09722.03823.3270.0583-0.15570.01050.235-0.30960.34090.282-0.26070.27950.2548-0.03180.06040.281-0.0470.2516-19.7938-23.99837.0402
184.83151.36211.11943.01522.59314.32030.0240.0684-0.1412-0.0335-0.41210.34550.0019-0.35910.39580.27480.00590.03360.2758-0.04690.2892-24.1774-31.023430.1801
190.99561.08330.85351.86171.34771.3817-0.0225-0.043-0.0661-0.01980.0149-0.04980.03270.0388-0.06810.2889-0.00090.03790.20760.01460.2431-20.0591-39.726617.9788
201.47690.0358-0.44343.14642.1143.21370.04630.0899-0.21910.05290.05210.08450.2633-0.0481-0.05890.3403-0.029-0.00110.28630.00140.3089-27.311-52.19799.2657
213.63341.17660.193.98292.5114.58110.0294-0.1253-0.09490.47910.088-0.19070.30420.1924-0.20040.36510.01340.02430.25880.06480.2299-24.8571-50.318811.9678
228.24290.6384-2.12132.16353.84279.0167-0.2180.3578-0.53050.27230.3988-0.46360.88350.72840.00240.51270.02660.06420.2489-0.00430.3664-18.1029-57.2958-2.0582
234.5031-1.1294-3.94693.23331.66476.6876-0.4240.5517-0.48640.0601-0.12570.32020.7854-0.66980.60040.3582-0.12150.00240.3027-0.04780.3284-32.1325-57.29313.6862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 30 )C1 - 30
2X-RAY DIFFRACTION2chain 'C' and (resid 31 through 62 )C31 - 62
3X-RAY DIFFRACTION3chain 'C' and (resid 63 through 99 )C63 - 99
4X-RAY DIFFRACTION4chain 'C' and (resid 100 through 111 )C100 - 111
5X-RAY DIFFRACTION5chain 'C' and (resid 112 through 201 )C112 - 201
6X-RAY DIFFRACTION6chain 'C' and (resid 202 through 213 )C202 - 213
7X-RAY DIFFRACTION7chain 'H' and (resid 1 through 17 )H1 - 17
8X-RAY DIFFRACTION8chain 'H' and (resid 18 through 72 )H18 - 72
9X-RAY DIFFRACTION9chain 'H' and (resid 73 through 98 )H73 - 98
10X-RAY DIFFRACTION10chain 'H' and (resid 99 through 109 )H99 - 109
11X-RAY DIFFRACTION11chain 'H' and (resid 110 through 125 )H110 - 125
12X-RAY DIFFRACTION12chain 'H' and (resid 126 through 151 )H126 - 151
13X-RAY DIFFRACTION13chain 'H' and (resid 152 through 163 )H152 - 163
14X-RAY DIFFRACTION14chain 'H' and (resid 164 through 190 )H164 - 190
15X-RAY DIFFRACTION15chain 'H' and (resid 191 through 219 )H191 - 219
16X-RAY DIFFRACTION16chain 'L' and (resid 1 through 25 )L1 - 25
17X-RAY DIFFRACTION17chain 'L' and (resid 26 through 81 )L26 - 81
18X-RAY DIFFRACTION18chain 'L' and (resid 82 through 96 )L82 - 96
19X-RAY DIFFRACTION19chain 'L' and (resid 97 through 134 )L97 - 134
20X-RAY DIFFRACTION20chain 'L' and (resid 135 through 156 )L135 - 156
21X-RAY DIFFRACTION21chain 'L' and (resid 157 through 180 )L157 - 180
22X-RAY DIFFRACTION22chain 'L' and (resid 181 through 194 )L181 - 194
23X-RAY DIFFRACTION23chain 'L' and (resid 195 through 217 )L195 - 217

+
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