[English] 日本語
Yorodumi
- PDB-6gkd: human NBD1 of CFTR in complex with nanobodies D12 and G3a -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gkd
Titlehuman NBD1 of CFTR in complex with nanobodies D12 and G3a
Components
  • Cystic fibrosis transmembrane conductance regulator
  • Nanobody D12
  • Nanobody G3a
KeywordsHYDROLASE / Cystic Fibrosis / CFTR / nanobodies / thermal stabilization / conformational dynamics
Function / homology
Function and homology information


positive regulation of voltage-gated chloride channel activity / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / positive regulation of enamel mineralization / transepithelial water transport / RHO GTPases regulate CFTR trafficking / intracellular pH elevation / ATPase-coupled inorganic anion transmembrane transporter activity ...positive regulation of voltage-gated chloride channel activity / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / positive regulation of enamel mineralization / transepithelial water transport / RHO GTPases regulate CFTR trafficking / intracellular pH elevation / ATPase-coupled inorganic anion transmembrane transporter activity / amelogenesis / chloride channel inhibitor activity / Golgi-associated vesicle membrane / multicellular organismal-level water homeostasis / vesicle docking involved in exocytosis / cholesterol transport / membrane hyperpolarization / bicarbonate transmembrane transporter activity / bicarbonate transport / chloride channel regulator activity / chloride transmembrane transporter activity / sperm capacitation / chloride channel activity / cholesterol biosynthetic process / RHOQ GTPase cycle / positive regulation of exocytosis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / chloride channel complex / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / cellular response to forskolin / cellular response to cAMP / isomerase activity / chloride transmembrane transport / response to endoplasmic reticulum stress / PDZ domain binding / establishment of localization in cell / Defective CFTR causes cystic fibrosis / clathrin-coated endocytic vesicle membrane / Late endosomal microautophagy / ABC-family proteins mediated transport / transmembrane transport / recycling endosome / Aggrephagy / Chaperone Mediated Autophagy / recycling endosome membrane / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / protein-folding chaperone binding / early endosome membrane / early endosome / endosome membrane / Ub-specific processing proteases / apical plasma membrane / lysosomal membrane / endoplasmic reticulum membrane / enzyme binding / cell surface / ATP hydrolysis activity / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
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
surcrose isoform / ADENOSINE-5'-TRIPHOSPHATE / Cystic fibrosis transmembrane conductance regulator / Cystic fibrosis transmembrane conductance regulator
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsSigoillot, M. / Overtus, M. / Grodecka, M. / Scholl, D. / Garcia-Pino, A. / Laeremans, T. / He, L. / Pardon, E. / Hildebrandt, E. / Urbatsch, I. ...Sigoillot, M. / Overtus, M. / Grodecka, M. / Scholl, D. / Garcia-Pino, A. / Laeremans, T. / He, L. / Pardon, E. / Hildebrandt, E. / Urbatsch, I. / Steyaert, J. / Riordan, J.R. / Govaerts, C.
CitationJournal: Nat Commun / Year: 2019
Title: Domain-interface dynamics of CFTR revealed by stabilizing nanobodies.
Authors: Sigoillot, M. / Overtus, M. / Grodecka, M. / Scholl, D. / Garcia-Pino, A. / Laeremans, T. / He, L. / Pardon, E. / Hildebrandt, E. / Urbatsch, I. / Steyaert, J. / Riordan, J.R. / Govaerts, C.
History
DepositionMay 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: diffrn_source / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cystic fibrosis transmembrane conductance regulator
B: Nanobody D12
C: Nanobody G3a
F: Cystic fibrosis transmembrane conductance regulator
G: Nanobody D12
H: Nanobody G3a
I: Cystic fibrosis transmembrane conductance regulator
J: Nanobody D12
K: Nanobody G3a
L: Cystic fibrosis transmembrane conductance regulator
M: Nanobody D12
N: Nanobody G3a
O: Cystic fibrosis transmembrane conductance regulator
P: Nanobody D12
Q: Nanobody G3a
R: Cystic fibrosis transmembrane conductance regulator
S: Nanobody D12
T: Nanobody G3a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,28141
Polymers349,09918
Non-polymers5,18223
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41190 Å2
ΔGint-264 kcal/mol
Surface area98410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.940, 146.830, 188.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Antibody , 2 types, 12 molecules BGJMPSCHKNQT

#2: Antibody
Nanobody D12


Mass: 16273.939 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Antibody
Nanobody G3a


Mass: 16383.900 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

-
Protein / Sugars , 2 types, 11 molecules AFILOR

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


Mass: 25525.408 Da / Num. of mol.: 6 / Mutation: del405-436
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFTR / Production host: Escherichia coli (E. coli)
References: UniProt: Q20BJ8, UniProt: P13569*PLUS, EC: 3.6.3.49
#4: Polysaccharide
alpha-D-fructofuranose-(2-1)-alpha-D-glucopyranose / surcrose isoform


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 342.297 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: surcrose isoform
DescriptorTypeProgram
DFrufa2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2a_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 244 molecules

#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.992→34.43 Å / Num. obs: 65508 / % possible obs: 99 % / Redundancy: 6.7 % / Biso Wilson estimate: 85.4 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.155 / Rrim(I) all: 0.1761 / Net I/σ(I): 11.4
Reflection shellResolution: 2.992→3.099 Å / Rmerge(I) obs: 1.106 / CC1/2: 0.4 / Rrim(I) all: 1.268

-
Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→34.43 Å / Cor.coef. Fo:Fc: 0.9154 / Cor.coef. Fo:Fc free: 0.8908 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.371
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 3276 5 %RANDOM
Rwork0.2044 ---
obs0.1927 65508 99.01 %-
Displacement parametersBiso mean: 75.86 Å2
Baniso -1Baniso -2Baniso -3
1--10.5218 Å20 Å20 Å2
2--15.873 Å20 Å2
3----5.3513 Å2
Refine analyzeLuzzati coordinate error obs: 0.413 Å
Refinement stepCycle: 1 / Resolution: 2.99→34.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20360 0 323 234 20917
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00921087HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0928688HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6936SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes398HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3254HARMONIC5
X-RAY DIFFRACTIONt_it21087HARMONIC20
X-RAY DIFFRACTIONt_nbd9SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion19.58
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2880SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact23073SEMIHARMONIC4
LS refinement shellResolution: 2.99→3.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3525 214 5.02 %
Rwork0.3206 4052 -
all0.2531 4266 -
obs--99.01 %
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)
12.2012-0.5462-0.25720.2760.22120.03040.00670.020.0279-0.01160.0045-0.05850.0161-0.0048-0.0112-0.0540.05060.08840.0135-0.00420.051-14.7222-12.36942.5713
20.64381.2105-0.3971.9339-0.9180.62540.004-0.00360.009-0.05010.0193-0.01950.06060.0014-0.0233-0.05550.0363-0.0284-0.0503-0.11650.0839-25.6191-36.706845.8776
31.2585-0.0534-0.16620.71540.09570.5080.01420.0542-0.0263-0.01360.0034-0.0005-0.0433-0.0449-0.01760.02480.0614-0.04030.0150.0256-0.0268-52.0256-1.199332.5708
40.1427-0.17480.15650.11410.01820.0079-0.0077-0.0008-0.01230.03340.0422-0.0347-0.008-0.0079-0.0344-0.01180.00620.0186-0.0079-0.00570.0095-36.941-2.266666.3504
50.03350.3606-0.75360.29010.84872.3085-0.01040.08410.06230.09120.0224-0.02960.04040.0207-0.0120.10760.1104-0.0025-0.0249-0.0794-0.1007-59.39468.202790.3321
60.74960.134-1.22352.54060.86540.49260.00440.01170.06180.01610.00390.0061-0.0019-0.0047-0.00820.11240.06570.079-0.0794-0.1167-0.033-51.019732.557684.6293
71.18880.52310.64451.4307-0.66981.1195-0.0068-0.00540.0106-0.0342-0.00220.0449-0.00080.00190.0090.0030.0225-0.0794-0.02640.02250.0191-70.21486.892551.7085
82.93870.048-0.31760.29510.34240-0.0021-0.02470.01180.04140.00480.0583-0.04380.0317-0.00270.00130.00280.0040.01910.0393-0.0101-67.4137-16.33770.9043
90.65260.8826-0.18690.8573-0.38461.28980.00030.03820.0148-0.0210.05520.03330.010.0051-0.0555-0.0186-0.0483-0.1003-0.03660.00680.0545-66.8212-21.566245.3221
101.0244-0.14680.05370.8995-0.52730.77650.0055-0.026-0.08070.0134-0.0093-0.0183-0.00820.01040.0037-0.02230.0732-0.1406-0.05-0.03290.0733-34.2605-38.375572.2071
110.45280.4867-0.94270.5450.15942.29940.0037-0.02670.0639-0.05010.0648-0.0330.0139-0.0158-0.06840.0054-0.040.05710.01250.022-0.0644-29.209416.000638.8482
121.7677-0.64220.22172.12280.05760.05130.01790.0140.041-0.0438-0.0460.03740.03820.00820.02810.05010.0834-0.0221-0.05750.1087-0.0275-53.860626.239241.8653
131.31970.18220.76030.7090.46711.6482-0.0029-0.01930.01430.0032-0.0064-0.0277-0.0287-0.01480.00940.0449-0.0508-0.09070.0005-0.1333-0.0522-24.767431.837475.9157
141.23291.2194-0.26281.5488-0.60890.06750.00110.06150.04940.0017-0.0106-0.03360.06250.04290.0095-0.077-0.04410.01580.0333-0.02390.0387-6.544112.465761.2754
151.03470.47560.66200.29731.61830.0012-0.0350.00480.0060.0013-0.01880.01080.0299-0.00240.0058-0.1091-0.08850.0284-0.0371-0.0234-4.869514.090187.4286
160.95990.14490.65151.419-0.15470.35420.01180.0166-0.0220.0587-0.0104-0.02480.01610.0048-0.0014-0.00290.0585-0.1007-0.0606-0.01960.0808-9.1732-27.462268.1248
170.35620.5046-0.75221.8803-0.58380.6030.0074-0.06460.02290.0238-0.0020.020.0109-0.0285-0.00550.0761-0.017-0.0510.00190.1077-0.0967-44.708-20.681493.4447
180.9582-0.3671.53920.0949-1.68850.69150.0033-0.0298-0.009-0.00690.015-0.00380.02780.028-0.01830.02410.013-0.1918-0.02930.1062-0.0049-18.655-27.010593.8701
190.33050.8618-0.25011.5220.26721.13950.003-0.00050.01930.0121-0.0104-0.0486-0.0308-0.02010.00750.0953-0.0712-0.0951-0.0621-0.0625-0.0507-30.790116.681797.7488
200.0091-0.28520.03520.04050.535200.0002-0.00010.0036-0.00990.00130.00160.00860.0015-0.00150.00530.0026-0.0046-0.00110.0005-0.0007-40.4364-7.071370.0148
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ F|* }
6X-RAY DIFFRACTION6{ G|* }
7X-RAY DIFFRACTION7{ H|* }
8X-RAY DIFFRACTION8{ I|* }
9X-RAY DIFFRACTION9{ J|* }
10X-RAY DIFFRACTION10{ K|* }
11X-RAY DIFFRACTION11{ L|* }
12X-RAY DIFFRACTION12{ M|* }
13X-RAY DIFFRACTION13{ N|* }
14X-RAY DIFFRACTION14{ O|* }
15X-RAY DIFFRACTION15{ P|* }
16X-RAY DIFFRACTION16{ Q|* }
17X-RAY DIFFRACTION17{ R|* }
18X-RAY DIFFRACTION18{ S|* }
19X-RAY DIFFRACTION19{ T|* }
20X-RAY DIFFRACTION20{ V|* }

+
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