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- PDB-3zx0: NTPDase1 in complex with Heptamolybdate -

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Basic information

Entry
Database: PDB / ID: 3zx0
TitleNTPDase1 in complex with Heptamolybdate
ComponentsECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
KeywordsHYDROLASE / DOMAIN ROTATION / POLYOXOMETALLATE / METAL CLUSTER / PURINERGIC SIGNALING
Function / homology
Function and homology information


response to proline / CDP phosphatase activity / ITPase activity / apyrase / apyrase activity / purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / nucleoside diphosphate catabolic process / nucleoside diphosphate phosphatase activity / UDP phosphatase activity ...response to proline / CDP phosphatase activity / ITPase activity / apyrase / apyrase activity / purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / nucleoside diphosphate catabolic process / nucleoside diphosphate phosphatase activity / UDP phosphatase activity / IDP phosphatase activity / cellular response to aluminum ion / GDP phosphatase activity / CTPase activity / ADP phosphatase activity / ADP catabolic process / cellular response to interferon-alpha / negative regulation of dopamine secretion / response to L-arginine / negative regulation of ATP biosynthetic process / response to auditory stimulus / response to caffeine / response to ATP / basement membrane / ribonucleoside triphosphate phosphatase activity / synaptic membrane / caveola / response to gamma radiation / platelet aggregation / platelet activation / synaptic vesicle / cellular response to tumor necrosis factor / basolateral plasma membrane / cellular response to lipopolysaccharide / response to lipopolysaccharide / G protein-coupled receptor signaling pathway / external side of plasma membrane / GTPase activity / neuronal cell body / cell surface / ATP hydrolysis activity / extracellular space / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
GDA1/CD39 family of nucleoside phosphatases signature. / Exopolyphosphatase. Domain 2 / Nucleoside phosphatase GDA1/CD39 / GDA1/CD39 (nucleoside phosphatase) family / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Chem-MO7 / Ectonucleoside triphosphate diphosphohydrolase 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZebisch, M. / Schaefer, P. / Straeter, N.
CitationJournal: J. Mol. Biol. / Year: 2012
Title: Crystallographic evidence for a domain motion in rat nucleoside triphosphate diphosphohydrolase (NTPDase) 1.
Authors: Zebisch, M. / Krauss, M. / Schafer, P. / Strater, N.
History
DepositionAug 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 2.0Jan 30, 2019Group: Atomic model / Data collection / Database references / Category: atom_site / citation
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 2.1Dec 20, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
B: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
C: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
D: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,88641
Polymers202,3724
Non-polymers5,51537
Water0
1
A: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
B: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,81917
Polymers101,1862
Non-polymers2,63315
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
D: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,06724
Polymers101,1862
Non-polymers2,88122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)163.807, 80.267, 164.921
Angle α, β, γ (deg.)90.00, 117.92, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A46 - 171
2113B46 - 171
3113C46 - 171
4113D46 - 171
1123A172 - 190
2123B172 - 190
3123C172 - 190
4123D172 - 190
1224A442 - 462
2224B442 - 462
3224C442 - 462
4224D442 - 462
1133A205 - 227
2133B205 - 227
3133C205 - 227
4133D205 - 227
1234A235 - 441
2234B235 - 441
3234C235 - 441
4234D235 - 441

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.905536, 0.418689, 0.068588), (0.366288, 0.68992, 0.624375), (0.214098, 0.590517, -0.778108)33.50219, -47.43243, 139.99446
3given(-0.995601, 0.023051, 0.090817), (-0.076128, -0.764064, -0.640633), (0.054623, -0.644728, 0.762458)41.47931, 46.15157, 95.8955
4given(0.935875, -0.268297, -0.228376), (-0.256671, -0.963203, 0.079747), (-0.241369, -0.016015, -0.970301)12.00969, 49.11057, 100.27267

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Components

#1: Protein
ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1 / NTPDASE 1 / ECTO-ATP DIPHOSPHOHYDROLASE 1 / ECTO-ATPDASE 1 / ECTO-ATPASE 1 / ECTO-APYRASE / ...NTPDASE 1 / ECTO-ATP DIPHOSPHOHYDROLASE 1 / ECTO-ATPDASE 1 / ECTO-ATPASE 1 / ECTO-APYRASE / LYMPHOID CELL ACTIVATION ANTIGEN / CD39


Mass: 50592.953 Da / Num. of mol.: 4 / Fragment: ECTODOMAIN, RESIDUES 38-189,206-477
Source method: isolated from a genetically manipulated source
Details: A PUTATIVE MEMBRANE INTERACTION LOOP 190TQEQSWLNFISDSQKQA206 WAS REPLACED BY A SHORTER LINKER KTPGGS
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PET45B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P97687, apyrase
#2: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical
ChemComp-MO7 / bis(mu4-oxo)-bis(mu3-oxo)-octakis(mu2-oxo)-dodecaoxo-heptamolybdenum (VI) / HEPTAMOLYBDATE [Mo(VI)7O24]6-


Mass: 1055.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mo7O24
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
Sequence detailsTHE LOOP T190 TO A206 WAS REPLACED WITH THE SEQUENCE KTPGGS OF GB EDL94186.1. THE RESIDUES 80, 220, ...THE LOOP T190 TO A206 WAS REPLACED WITH THE SEQUENCE KTPGGS OF GB EDL94186.1. THE RESIDUES 80, 220, AND 227 MATCH THE GENBANK SEQUENCE.

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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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 4.2 / Details: 3.8M NACL, 100MM NAACETAT PH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.89461
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89461 Å / Relative weight: 1
ReflectionResolution: 2.5→29.15 Å / Num. obs: 57453 / % possible obs: 87.6 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 65.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.7
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2 / % possible all: 28.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CJ1
Resolution: 2.5→145.73 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 25.855 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R: 0.773 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25718 1157 2 %RANDOM
Rwork0.21336 ---
obs0.21426 56295 87.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.46 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å2-0.61 Å2
2--3.73 Å20 Å2
3----5.35 Å2
Refinement stepCycle: LAST / Resolution: 2.5→145.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12189 0 178 0 12367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212793
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5442.02417535
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.07251559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3424.49539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.055152059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.4391525
X-RAY DIFFRACTIONr_chiral_restr0.120.21819
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219564
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
21A141medium positional0.690.5
22B141medium positional0.70.5
23C141medium positional0.470.5
24D141medium positional0.440.5
31A1540medium positional0.410.5
32B1540medium positional0.410.5
33C1540medium positional0.380.5
34D1540medium positional0.340.5
11A408loose positional0.085
12B408loose positional0.085
13C408loose positional0.095
14D408loose positional0.145
21A80loose positional0.735
22B80loose positional0.985
23C80loose positional0.635
24D80loose positional0.615
31A58loose positional0.565
32B58loose positional0.315
33C58loose positional0.285
34D58loose positional0.315
11A459tight thermal2.110.5
12B459tight thermal1.480.5
13C459tight thermal1.570.5
14D459tight thermal1.930.5
21A76tight thermal0.920.5
22B76tight thermal1.750.5
23C76tight thermal1.550.5
24D76tight thermal1.640.5
31A88tight thermal1.470.5
32B88tight thermal2.40.5
33C88tight thermal1.760.5
34D88tight thermal2.410.5
21A141medium thermal3.622
22B141medium thermal2.932
23C141medium thermal1.812
24D141medium thermal2.352
31A1540medium thermal3.272
32B1540medium thermal2.912
33C1540medium thermal2.92
34D1540medium thermal2.642
11A408loose thermal2.7410
12B408loose thermal2.3510
13C408loose thermal2.1110
14D408loose thermal3.810
21A80loose thermal1.7910
22B80loose thermal2.6210
23C80loose thermal1.9610
24D80loose thermal2.3510
31A58loose thermal1.4310
32B58loose thermal3.1510
33C58loose thermal2.0410
34D58loose thermal2.2910
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 16 -
Rwork0.301 709 -
obs--15.03 %
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)
15.4472.0278-1.97565.7018-1.39345.2832-0.61180.3749-0.6877-0.32190.0635-0.50751.57430.01030.54830.9849-0.17040.13790.8152-0.08550.466132.1883-9.897396.8742
24.7516-2.16993.12515.4577-3.93548.8636-0.11040.6232-0.4608-0.37560.05530.10941.6915-0.69690.05510.8037-0.51330.0561.0889-0.16070.479914.6563-5.379395.9533
34.47381.45311.4431.69531.14215.6369-0.40540.67550.3177-0.26190.35210.2143-0.184-0.84180.05330.4493-0.0304-0.09040.62610.10580.402523.757114.6418103.9925
46.05990.8487-0.81054.47941.58968.9037-0.3988-0.0177-0.7284-0.24660.06260.21840.9998-0.83190.33620.6898-0.11790.22250.45890.17590.6145.9432-0.404956.7012
59.03983.44761.94124.5169-0.32695.6903-0.4638-0.4358-1.8232-0.46470.297-0.63421.0443-0.18720.16680.85550.16230.34570.43310.24591.043622.842-4.242159.2769
62.6820.0663-0.88244.6032-1.32265.1792-0.0557-0.9161-0.2824-0.0421-0.0403-0.4382-0.27470.52360.0960.46290.05720.04920.6050.04660.479422.90418.482765.267
74.64940.61371.29673.93221.72767.4008-0.003-0.3230.57450.7833-0.11640.3583-0.863-0.96680.11950.9030.18520.19690.33090.02340.461513.870542.162935.7798
811.3437-0.4387-0.01775.24841.15210.93750.3146-0.11831.02041.0159-0.2101-0.5805-0.995-0.0206-0.10450.7454-0.0457-0.04170.03780.03980.461830.569139.394930.3068
92.70310.6599-2.04552.3093-1.47564.8483-0.16650.2638-0.15720.28920.050.09760.3979-0.48060.11650.4078-0.00580.03540.171-0.03030.336520.333818.470225.0924
102.78360.8831-0.67585.6882-1.13513.40540.06240.12020.3586-0.0215-0.1986-0.3671-0.29720.10720.13630.16-0.0174-0.05240.37870.06620.305234.501352.0865-5.896
118.9117-1.4117-3.0754.8702-2.35837.51960.3341-0.1560.88610.21260.00610.4374-0.9194-0.5185-0.34020.25390.1146-0.03850.37480.0190.44417.787651.701-0.7812
121.58910.2397-0.84672.55240.10115.9348-0.17120.2531-0.1581-0.32020.05270.20620.5475-0.73560.11850.2176-0.1298-0.06390.46590.03680.386519.494630.1503-9.9186
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 171
2X-RAY DIFFRACTION2A172 - 190
3X-RAY DIFFRACTION2A442 - 462
4X-RAY DIFFRACTION3A205 - 441
5X-RAY DIFFRACTION4B46 - 171
6X-RAY DIFFRACTION5B172 - 190
7X-RAY DIFFRACTION5B442 - 466
8X-RAY DIFFRACTION6B205 - 441
9X-RAY DIFFRACTION7C47 - 171
10X-RAY DIFFRACTION8C172 - 190
11X-RAY DIFFRACTION8C442 - 465
12X-RAY DIFFRACTION9C205 - 441
13X-RAY DIFFRACTION10D46 - 171
14X-RAY DIFFRACTION11D172 - 190
15X-RAY DIFFRACTION11D442 - 463
16X-RAY DIFFRACTION12D205 - 441

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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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