[English] 日本語
Yorodumi
- PDB-3si7: The crystal structure of the NBD1 domain of the mouse CFTR protei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3si7
TitleThe crystal structure of the NBD1 domain of the mouse CFTR protein, deltaF508 mutant
ComponentsCystic fibrosis transmembrane conductance regulator
KeywordsHYDROLASE / cystic fibrosis / ATP-binding domain
Function / homology
Function and homology information


RHO GTPases regulate CFTR trafficking / RHOQ GTPase cycle / positive regulation of mast cell activation / transepithelial chloride transport / positive regulation of establishment of Sertoli cell barrier / Aggrephagy / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity ...RHO GTPases regulate CFTR trafficking / RHOQ GTPase cycle / positive regulation of mast cell activation / transepithelial chloride transport / positive regulation of establishment of Sertoli cell barrier / Aggrephagy / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / water transport / positive regulation of enamel mineralization / transepithelial water transport / negative regulation of vascular associated smooth muscle cell apoptotic process / intracellular pH elevation / enamel mineralization / negative regulation of type B pancreatic cell development / amelogenesis / chloride channel inhibitor activity / Cargo recognition for clathrin-mediated endocytosis / ABC-family proteins mediated transport / Clathrin-mediated endocytosis / multicellular organismal-level water homeostasis / vesicle docking involved in exocytosis / Ub-specific processing proteases / membrane hyperpolarization / cholesterol transport / bicarbonate transport / bicarbonate transmembrane transporter activity / chloride transport / chloride transmembrane transporter activity / sperm capacitation / chloride channel activity / cholesterol biosynthetic process / positive regulation of exocytosis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / microvillus / chloride channel complex / ATPase-coupled transmembrane transporter activity / sodium ion transmembrane transport / ABC-type transporter activity / cellular response to cAMP / cellular response to forskolin / isomerase activity / chloride transmembrane transport / response to endoplasmic reticulum stress / establishment of localization in cell / PDZ domain binding / lung development / recycling endosome membrane / vasodilation / protein-folding chaperone binding / early endosome membrane / basolateral plasma membrane / early endosome / response to xenobiotic stimulus / apical plasma membrane / neuronal cell body / dendrite / endoplasmic reticulum membrane / enzyme binding / cell surface / ATP hydrolysis activity / ATP binding / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
: / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. ...: / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-TRIPHOSPHATE / Cystic fibrosis transmembrane conductance regulator
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 Å
AuthorsBrautigam, C.A. / Caspa, E. / Thomas, P.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Requirements for efficient correction of DeltaF508 CFTR revealed by analyses of evolved sequences
Authors: Mendoza, J.L. / Schmidt, A. / Li, Q. / Nuvaga, E. / Barrett, T. / Bridges, R.J. / Feranchak, A.P. / Brautigam, C.A. / Thomas, P.J.
History
DepositionJun 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cystic fibrosis transmembrane conductance regulator
B: Cystic fibrosis transmembrane conductance regulator
C: Cystic fibrosis transmembrane conductance regulator
D: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,44123
Polymers127,8054
Non-polymers2,63619
Water5,242291
1
A: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6256
Polymers31,9511
Non-polymers6745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5665
Polymers31,9511
Non-polymers6154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6256
Polymers31,9511
Non-polymers6745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6256
Polymers31,9511
Non-polymers6745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Cystic fibrosis transmembrane conductance regulator
B: Cystic fibrosis transmembrane conductance regulator
hetero molecules

A: Cystic fibrosis transmembrane conductance regulator
B: Cystic fibrosis transmembrane conductance regulator
hetero molecules

A: Cystic fibrosis transmembrane conductance regulator
B: Cystic fibrosis transmembrane conductance regulator
hetero molecules

A: Cystic fibrosis transmembrane conductance regulator
B: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,76444
Polymers255,6098
Non-polymers5,15536
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation7_646y+1,x-1,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area29940 Å2
ΔGint-255 kcal/mol
Surface area79430 Å2
MethodPISA
6
C: Cystic fibrosis transmembrane conductance regulator
D: Cystic fibrosis transmembrane conductance regulator
hetero molecules

C: Cystic fibrosis transmembrane conductance regulator
D: Cystic fibrosis transmembrane conductance regulator
hetero molecules

C: Cystic fibrosis transmembrane conductance regulator
D: Cystic fibrosis transmembrane conductance regulator
hetero molecules

C: Cystic fibrosis transmembrane conductance regulator
D: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,00048
Polymers255,6098
Non-polymers5,39140
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area28160 Å2
ΔGint-256 kcal/mol
Surface area83270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.546, 170.546, 109.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

-
Components

#1: Protein
Cystic fibrosis transmembrane conductance regulator / / CFTR / ATP-binding cassette sub-family C member 7 / Channel conductance-controlling ATPase / cAMP- ...CFTR / ATP-binding cassette sub-family C member 7 / Channel conductance-controlling ATPase / cAMP-dependent chloride channel


Mass: 31951.152 Da / Num. of mol.: 4 / Fragment: Nucleotide-binding domain 1, UNP residues 389-673
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cftr, Abcc7 / Production host: Escherichia coli (E. coli) / References: UniProt: P26361, EC: 3.6.3.49
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5 M Sodium Acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97156 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97156 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 76676 / Num. obs: 76676 / % possible obs: 100 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.25→2.28 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIX(phenix.refine: 1.7_650)model building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.25→49.9 Å / SU ML: 0.35 / σ(F): 0 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 3847 5.02 %random
Rwork0.1815 ---
obs0.1838 76625 99.94 %-
all-76676 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.483 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3017 Å20 Å2-0 Å2
2--0.3017 Å20 Å2
3----0.6034 Å2
Refinement stepCycle: LAST / Resolution: 2.25→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8318 0 160 291 8769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078635
X-RAY DIFFRACTIONf_angle_d1.07611640
X-RAY DIFFRACTIONf_dihedral_angle_d14.1373197
X-RAY DIFFRACTIONf_chiral_restr0.0691309
X-RAY DIFFRACTIONf_plane_restr0.0031458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.27890.26891340.24242675X-RAY DIFFRACTION100
2.2789-2.30890.22861320.20482640X-RAY DIFFRACTION100
2.3089-2.34050.2561530.20062663X-RAY DIFFRACTION100
2.3405-2.37390.29051230.22162664X-RAY DIFFRACTION100
2.3739-2.40940.28631390.22222664X-RAY DIFFRACTION100
2.4094-2.4470.29971450.23112655X-RAY DIFFRACTION100
2.447-2.48710.2941600.21762634X-RAY DIFFRACTION100
2.4871-2.530.28991390.21662679X-RAY DIFFRACTION100
2.53-2.5760.29131400.21682660X-RAY DIFFRACTION100
2.576-2.62550.32381530.21762661X-RAY DIFFRACTION100
2.6255-2.67910.27261500.21342657X-RAY DIFFRACTION100
2.6791-2.73740.2651400.20832681X-RAY DIFFRACTION100
2.7374-2.80110.2191470.19972686X-RAY DIFFRACTION100
2.8011-2.87110.26361400.20192651X-RAY DIFFRACTION100
2.8711-2.94870.23841430.20932673X-RAY DIFFRACTION100
2.9487-3.03550.2381360.21332698X-RAY DIFFRACTION100
3.0355-3.13340.25281470.20072681X-RAY DIFFRACTION100
3.1334-3.24540.2431400.18872678X-RAY DIFFRACTION100
3.2454-3.37530.21341360.18812717X-RAY DIFFRACTION100
3.3753-3.52890.22191410.17572696X-RAY DIFFRACTION100
3.5289-3.71490.20931300.16612717X-RAY DIFFRACTION100
3.7149-3.94760.19661510.1582705X-RAY DIFFRACTION100
3.9476-4.25220.18471480.14112716X-RAY DIFFRACTION100
4.2522-4.67980.16641260.13782755X-RAY DIFFRACTION100
4.6798-5.35630.21781530.14832767X-RAY DIFFRACTION100
5.3563-6.74580.22521360.19382802X-RAY DIFFRACTION100
6.7458-49.90.22111650.1862903X-RAY DIFFRACTION99
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)
10.69250.2753-0.24680.64240.21480.26290.2113-0.38860.00550.0332-0.1176-0.3783-0.20560.1726-0.03110.4302-0.092-0.13830.53870.02170.579152.94617.912432.8343
20.17830.00040.01890.3645-0.01620.2988-0.05960.15020.1880.2246-0.08910.1164-0.1532-0.1820.06940.24370.0103-0.0390.3919-0.07640.3313145.42826.303634.3526
30.2711-0.0837-0.15420.31990.19670.14440.05850.21830.012-0.1618-0.19220.27190.0232-0.0824-0.02240.1901-0.0178-0.04240.3801-0.10550.2319145.4703-1.927725.506
40.390.0554-0.37181.4122-0.75940.70930.02420.09160.1198-0.2557-0.1593-0.32130.02870.27570.1010.28670.00130.03290.67810.0810.3004161.92044.518414.8599
50.21220.080.06170.26830.07190.0313-0.08350.22850.02690.02360.3699-0.0406-0.063-0.1671-0.12820.6029-0.0697-0.00220.96940.0070.318141.25173.024654.121
60.9686-0.32960.18410.8599-0.54130.4307-0.56730.30660.05880.33580.2563-0.1925-0.1001-0.3753-0.41210.222-0.13450.27970.4324-0.06510.0662138.3104-7.12370.8163
70.00510.00150.0130.0224-0.00070.0304-0.03390.1066-0.1042-0.0550.049-0.03920.01020.02130.08190.468-0.28420.33310.5949-0.33640.4373138.7842-22.121658.4185
80.1086-0.0388-0.07310.31850.26780.2325-0.15230.0225-0.16520.0952-0.10910.4530.1416-0.02640.13420.55130.11380.13160.5046-0.04170.6622101.93858.67690.4662
90.49010.04850.19660.30160.04150.61840.10790.0413-0.0345-0.0819-0.044-0.0876-0.02030.00510.01250.20580.01360.08220.242-0.03980.2894116.9033-0.885496.0826
100.82580.1046-0.07150.23340.09590.76430.1092-0.12390.29040.0739-0.2205-0.0569-0.3149-0.0409-0.00780.3539-0.03880.10460.2867-0.08690.4531120.412515.1571106.7082
110.17560.1125-0.22860.7908-0.27460.31910.0250.0109-0.02880.1304-0.18610.1562-0.0642-0.12840.06320.4502-0.25810.06390.8534-0.00140.509697.0725-19.633635.4292
120.38630.20450.0140.7373-0.13420.8327-0.12130.09050.0433-0.0826-0.13270.1145-0.12190.04290.16260.70940.017-0.11970.9167-0.01340.674289.0089-13.943923.7285
130.2258-0.1306-0.21240.8826-0.17220.44060.134-0.2933-0.23640.3809-0.08110.33250.0639-0.3065-0.00050.3452-0.1721-0.00210.50630.04610.3115103.1855-19.483332.5073
140.8933-0.75440.31840.9438-0.43672.12590.3194-0.297-0.15610.10310.03060.2001-0.2591-0.228-0.13490.2903-0.02220.02520.3668-0.06290.3306114.8539-1.097720.991
150.2416-0.1382-0.14890.24130.15760.4310.1431-0.1452-0.02260.0558-0.05170.03780.0838-0.0921-0.00580.1847-0.0647-0.05390.25150.0020.3129116.1128-17.808720.9499
160.16150.3764-0.03421.3577-0.310.2264-0.05240.0972-0.1014-0.2509-0.0347-0.17370.1252-0.14070.05160.3196-0.1366-0.10810.3475-0.02780.4488106.3166-31.5413.21
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 390:452)
2X-RAY DIFFRACTION2chain 'A' and (resseq 453:512)
3X-RAY DIFFRACTION3chain 'A' and (resseq 513:636)
4X-RAY DIFFRACTION4chain 'A' and (resseq 637:669)
5X-RAY DIFFRACTION5chain 'B' and (resseq 389:436)
6X-RAY DIFFRACTION6chain 'B' and (resseq 437:644)
7X-RAY DIFFRACTION7chain 'B' and (resseq 645:669)
8X-RAY DIFFRACTION8chain 'C' and (resseq 388:436)
9X-RAY DIFFRACTION9chain 'C' and (resseq 437:644)
10X-RAY DIFFRACTION10chain 'C' and (resseq 645:669)
11X-RAY DIFFRACTION11chain 'D' and (resseq 390:404)
12X-RAY DIFFRACTION12chain 'D' and (resseq 405:436)
13X-RAY DIFFRACTION13chain 'D' and (resseq 437:491)
14X-RAY DIFFRACTION14chain 'D' and (resseq 492:512)
15X-RAY DIFFRACTION15chain 'D' and (resseq 513:645)
16X-RAY DIFFRACTION16chain 'D' and (resseq 646:669)

+
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