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- PDB-2wd0: CRYSTAL STRUCTURE OF NONSYNDROMIC DEAFNESS (DFNB12) ASSOCIATED MU... -

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Basic information

Entry
Database: PDB / ID: 2wd0
TitleCRYSTAL STRUCTURE OF NONSYNDROMIC DEAFNESS (DFNB12) ASSOCIATED MUTANT D124G OF MOUSE CADHERIN-23 EC1-2
ComponentsCADHERIN-23
KeywordsCELL ADHESION / HEARING
Function / homology
Function and homology information


cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / stereocilium ...cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / stereocilium / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / photoreceptor cell maintenance / catenin complex / auditory receptor cell stereocilium organization / inner ear morphogenesis / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / regulation of cytosolic calcium ion concentration / photoreceptor inner segment / locomotory behavior / sensory perception of sound / calcium ion transport / apical part of cell / cell adhesion / cadherin binding / centrosome / synapse / calcium ion binding / plasma membrane
Similarity search - Function
Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin-like ...Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsSotomayor, M. / Weihofen, W. / Gaudet, R. / Corey, D.P.
CitationJournal: Neuron / Year: 2010
Title: Structural Determinants of Cadherin-23 Function in Hearing and Deafness.
Authors: Sotomayor, M. / Weihofen, W. / Gaudet, R. / Corey, D.P.
History
DepositionMar 18, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CADHERIN-23
C: CADHERIN-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,99013
Polymers47,5972
Non-polymers39311
Water93752
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A: CADHERIN-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0137
Polymers23,7981
Non-polymers2146
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: CADHERIN-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9776
Polymers23,7981
Non-polymers1795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)179.693, 179.693, 63.982
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22C

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUVALVALAA6 - 1006 - 100
21LEULEUVALVALCB6 - 1006 - 100
12ASPASPTHRTHRAA105 - 205105 - 205
22ASPASPTHRTHRCB105 - 205105 - 205

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.99091, -0.13448, 0.00182), (-0.13408, 0.98675, -0.09139), (0.0105, -0.09081, -0.99581)2.19113, -0.11849, -5.55911
2given(-0.994, 0.023, 0.107), (0.011, 0.994, -0.11), (-0.109, -0.108, -0.988)-2.63817, 1.6686, -7.71249

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Components

#1: Protein CADHERIN-23 / / OTOCADHERIN


Mass: 23798.400 Da / Num. of mol.: 2 / Fragment: EC1-2, RESIDUES 24-228 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: AMINO-ACID NUMBERING ACCORDING TO SEQUENCE OF CRYSTALLIZED CONSTRUCT.
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99PF4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 124 TO GLY ENGINEERED RESIDUE IN CHAIN C, ASP 124 TO GLY
Sequence detailsRESIDUE ASPARTATE 124 (DATABASE NUMBERING) IS MUTATED TO GLYCINE.

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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: 5.38 Å3/Da / Density % sol: 77.15 % / Description: NONE
Crystal growpH: 7.1 / Details: 0.1M SODIUM CACODYLATE PH 7.1, 1M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 28267 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.8
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.47 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WCP
Resolution: 2.74→29.77 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.907 / SU B: 21.451 / SU ML: 0.185 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.316 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.24865 1384 5 %RANDOM
Rwork0.21941 ---
obs0.22089 26041 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: SIMPLE SCALING
Displacement parametersBiso mean: 23.276 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.74→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3248 0 11 52 3311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223360
X-RAY DIFFRACTIONr_bond_other_d0.0010.022172
X-RAY DIFFRACTIONr_angle_refined_deg1.0991.9464608
X-RAY DIFFRACTIONr_angle_other_deg0.835314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.675418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02524.819166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.09315498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5951518
X-RAY DIFFRACTIONr_chiral_restr0.0660.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213802
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02676
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4631.52096
X-RAY DIFFRACTIONr_mcbond_other0.0581.5828
X-RAY DIFFRACTIONr_mcangle_it0.87523444
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.99231264
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7434.51164
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1298loose positional0.455
12C1298loose positional0.455
21A1274loose positional0.495
22C1274loose positional0.495
11A1298loose thermal2.4510
12C1298loose thermal2.4510
21A1274loose thermal2.3710
22C1274loose thermal2.3710
LS refinement shellResolution: 2.744→2.814 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 99 -
Rwork0.358 1876 -
obs--97.58 %
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)
11.2550.05061.12292.81490.352.07020.180.2307-0.3714-0.4207-0.18770.1543-0.1364-0.35610.00780.26180.1454-0.12020.3793-0.24260.252-6.22711.649-22.864
24.711-1.5756-1.91493.06-0.31012.1304-0.32350.0093-0.20350.18510.1950.4331-0.1919-0.17510.12850.16550.05420.0180.04250.02780.1361-13.68721.442-3.808
31.2055-1.5159-2.63835.01030.43188.4578-0.07960.1592-0.20280.0449-0.29780.32480.2201-0.25470.37740.0223-0.01930.01690.0309-0.03210.0371-6.01710.964-14.91
43.4096-3.6247-1.78868.10574.48336.4093-0.22030.04780.1607-0.29060.21370.0843-0.24510.05780.00660.0923-0.0238-0.02890.02840.03010.0358-2.91221.295-16.255
59.142-5.3301-0.99054.70741.10732.0486-0.08760.01080.34930.09250.1164-0.1778-0.1775-0.083-0.02890.04590.01540.01040.0180.00140.0218-6.80725.534-5.539
63.3982-2.1647-3.1428.0853.90145.19110.08210.9077-0.0718-0.2869-0.31350.6519-0.4177-0.84440.23150.06480.0483-0.01410.310.01120.0766-13.23427.122-13.009
711.82820.5826-1.66461.0378-1.65162.6795-0.11850.12120.2296-0.0975-0.0717-0.13480.14730.1090.19020.047-0.01090.02590.01470.0070.03153.20416.07-24.036
81.6765-1.3232-1.51811.71621.10491.4647-0.0782-0.0541-0.1005-0.0372-0.00920.38740.06910.11390.08740.09950.0511-0.03730.08410.01610.1686-16.6627.936-6.198
98.7356-3.4606-4.51713.26051.58523.5017-0.0973-0.50540.26910.04860.2233-0.2427-0.17050.1235-0.1260.06030.0506-0.00990.0672-0.02570.0233-34.88655.50717.735
100.56850.1246-1.58721.3356-0.20634.6404-0.0537-0.1747-0.01120.04580.09380.1305-0.0170.4118-0.04020.16490.12370.05590.1745-0.01810.1388-29.44937.57810.163
113.2047-0.73742.88740.75420.74166.7486-0.1263-0.4571-0.05090.03870.1943-0.088-0.2861-0.2918-0.06810.11580.0714-0.01450.1031-0.01610.1069-35.30745.1924.263
123.65750.5906-0.97427.71151.98790.867-0.0826-0.351-0.17860.047-0.09760.42770.0280.06790.18020.0610.07140.00140.1060.00420.0418-40.79250.5922.249
131.7795-1.7443-0.63685.3142.12733.79440.0933-0.25820.09030.63160.0094-0.91560.2594-0.6086-0.10280.23490.0359-0.13780.28590.01440.2269-29.92144.31322.187
140.1391-0.559-0.07266.31151.5293.918-0.131-0.15010.10680.268-0.01540.0515-0.11520.21750.14640.20470.1641-0.05070.2873-0.19090.2455-26.18945.43918.956
1511.14569.473512.69018.058310.792714.4568-1.78071.66350.2727-1.49611.5150.2005-2.02821.97760.26570.67310.21870.14071.2808-0.34181.033-38.36566.74827.398
160.28541.12090.25297.1572-1.7032.97080.0233-0.1382-0.12020.5303-0.1371-0.5778-0.4762-0.35010.11380.14510.0017-0.09590.45010.21580.18969.08215.33814.297
174.25611.24680.55640.68580.23270.846-0.16960.27570.2166-0.17830.1792-0.1781-0.07350.1359-0.00960.1419-0.05560.11770.0563-0.05960.204110.59723.868-6.752
180.7553-0.24821.22020.84341.60587.25850.0968-0.0386-0.0778-0.0467-0.04670.05320.1197-0.2083-0.05020.0146-0.0073-0.01280.06390.02940.02256.90812.9647.645
192.8108-0.23442.51780.41790.72615.3719-0.1387-0.65260.1163-0.01860.2909-0.0667-0.4785-0.3909-0.15220.10340.11920.05950.4205-0.01740.08422.17922.7028.503
208.72295.2849-1.80227.3123-3.40862.38030.0359-0.42040.6423-0.0210.06710.4416-0.15480.1073-0.1030.0527-0.0527-0.00740.1037-0.00910.05535.40926.119-2.455
211.14990.8893-0.14312.7113-1.20694.77220.1868-0.70250.16390.7291-0.1005-0.5956-1.4261-0.0596-0.08640.4863-0.0059-0.0590.5322-0.26370.335911.62329.7074.809
222.5429-2.2301-1.84358.774-0.38221.92270.1546-0.09840.07920.065-0.00760.2449-0.17080.1047-0.1470.0177-0.01830.00850.2240.02820.0309-2.95317.70517.173
231.77171.1663-0.47692.3596-1.63871.3143-0.1309-0.13970.28170.15630.1404-0.02-0.1852-0.163-0.00950.1242-0.0017-0.0140.0783-0.05330.204115.69829.673-1.973
249.05652.8147-2.85743.7725-1.76273.72930.05480.31660.16160.12050.11870.3556-0.5334-0.1208-0.17350.11580.00670.04740.01540.01740.093935.10954.497-27.354
252.17441.9186-0.94681.6976-0.84130.4358-0.0847-0.041-0.1128-0.1002-0.0209-0.1060.06910.02730.10560.1352-0.07530.04010.09520.06460.155428.68337.569-18.725
263.04391.70380.60954.7134-4.00237.46150.04710.4089-0.1041-0.54130.39840.24530.01960.5434-0.44550.3247-0.17080.05740.26460.02270.150236.18143.503-32.786
274.08281.86-2.98886.1631-6.30627.35260.2448-0.012-0.08440.0598-0.1783-0.154-0.26730.1425-0.06640.05010.00570.0520.00840.0160.102841.44649.087-30.729
283.21193.0734-1.94478.4211-3.09112.6358-0.42790.44740.0898-0.72090.66120.42580.4434-0.4707-0.23330.136-0.1092-0.03340.10530.04230.040930.23143.197-31.333
291.15870.60271.40480.3620.8361.9361-0.22360.30920.2368-0.09650.06810.0698-0.21010.16880.15560.2044-0.1224-0.04030.26930.19340.223726.4244.398-28.509
302.4808-4.84320.60079.5785-1.63881.98140.067-0.01050.0264-0.170.0433-0.00790.1302-0.0269-0.11020.0865-0.03510.00640.05690.05090.081639.0564.874-37.963
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 14
2X-RAY DIFFRACTION1A504
3X-RAY DIFFRACTION2A15 - 30
4X-RAY DIFFRACTION3A31 - 36
5X-RAY DIFFRACTION4A37 - 56
6X-RAY DIFFRACTION5A57 - 75
7X-RAY DIFFRACTION6A76 - 84
8X-RAY DIFFRACTION7A85 - 89
9X-RAY DIFFRACTION8A90 - 110
10X-RAY DIFFRACTION8A501 - 502
11X-RAY DIFFRACTION8A601
12X-RAY DIFFRACTION9A111 - 133
13X-RAY DIFFRACTION10A134 - 149
14X-RAY DIFFRACTION11A150 - 161
15X-RAY DIFFRACTION12A162 - 172
16X-RAY DIFFRACTION13A173 - 192
17X-RAY DIFFRACTION14A193 - 203
18X-RAY DIFFRACTION15A204 - 208
19X-RAY DIFFRACTION16C2 - 17
20X-RAY DIFFRACTION16C504
21X-RAY DIFFRACTION17C18 - 30
22X-RAY DIFFRACTION18C31 - 36
23X-RAY DIFFRACTION19C37 - 56
24X-RAY DIFFRACTION20C57 - 75
25X-RAY DIFFRACTION21C76 - 84
26X-RAY DIFFRACTION22C85 - 89
27X-RAY DIFFRACTION23C90 - 110
28X-RAY DIFFRACTION23C501 - 503
29X-RAY DIFFRACTION23C601
30X-RAY DIFFRACTION24C111 - 133
31X-RAY DIFFRACTION25C134 - 149
32X-RAY DIFFRACTION26C150 - 161
33X-RAY DIFFRACTION27C162 - 172
34X-RAY DIFFRACTION28C173 - 192
35X-RAY DIFFRACTION29C193 - 203
36X-RAY DIFFRACTION30C204 - 208

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