[English] 日本語
Yorodumi
- PDB-6be6: ADAM10 Extracellular Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6be6
TitleADAM10 Extracellular Domain
ComponentsDisintegrin and metalloproteinase domain-containing protein 10
KeywordsMEMBRANE PROTEIN / ADAM10
Function / homology
Function and homology information


ADAM10 endopeptidase / constitutive protein ectodomain proteolysis / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / regulation of vasculature development / epidermal growth factor receptor ligand maturation / monocyte activation / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / postsynapse organization / protein catabolic process at postsynapse / positive regulation of T cell chemotaxis ...ADAM10 endopeptidase / constitutive protein ectodomain proteolysis / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / regulation of vasculature development / epidermal growth factor receptor ligand maturation / monocyte activation / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / postsynapse organization / protein catabolic process at postsynapse / positive regulation of T cell chemotaxis / perinuclear endoplasmic reticulum / tetraspanin-enriched microdomain / regulation of Notch signaling pathway / pore complex assembly / NOTCH4 Activation and Transmission of Signal to the Nucleus / metallodipeptidase activity / adherens junction organization / positive regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of cell adhesion / regulation of postsynapse organization / clathrin-coated vesicle / Golgi-associated vesicle / amyloid precursor protein catabolic process / Signaling by EGFR / pore complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Collagen degradation / membrane protein ectodomain proteolysis / response to tumor necrosis factor / tertiary granule membrane / extracellular matrix disassembly / cochlea development / EPH-ephrin mediated repulsion of cells / specific granule membrane / Notch signaling pathway / Degradation of the extracellular matrix / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / synaptic membrane / integrin-mediated signaling pathway / Post-translational protein phosphorylation / adherens junction / NOTCH3 Activation and Transmission of Signal to the Nucleus / protein processing / metalloendopeptidase activity / SH3 domain binding / integrin binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / epidermal growth factor receptor signaling pathway / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / metallopeptidase activity / positive regulation of tumor necrosis factor production / cell-cell signaling / positive regulation of cell growth / endopeptidase activity / in utero embryonic development / postsynaptic density / positive regulation of cell migration / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / negative regulation of gene expression / axon / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / dendrite / glutamatergic synapse / cell surface / Golgi apparatus / protein homodimerization activity / extracellular exosome / metal ion binding / membrane / plasma membrane
Similarity search - Function
ADAM10/ADAM17 catalytic domain / : / : / Metallo-peptidase family M12B Reprolysin-like / ADAM10, cysteine-rich domain / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily ...ADAM10/ADAM17 catalytic domain / : / : / Metallo-peptidase family M12B Reprolysin-like / ADAM10, cysteine-rich domain / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Disintegrin and metalloproteinase domain-containing protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSeegar, T.C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
CitationJournal: Cell / Year: 2017
Title: Structural Basis for Regulated Proteolysis by the alpha-Secretase ADAM10.
Authors: Seegar, T.C.M. / Killingsworth, L.B. / Saha, N. / Meyer, P.A. / Patra, D. / Zimmerman, B. / Janes, P.W. / Rubinstein, E. / Nikolov, D.B. / Skiniotis, G. / Kruse, A.C. / Blacklow, S.C.
History
DepositionOct 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _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_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_distant_solvent_atoms ...atom_site / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn
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_seq_id / _atom_site.label_asym_id / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Disintegrin and metalloproteinase domain-containing protein 10
B: Disintegrin and metalloproteinase domain-containing protein 10
C: Disintegrin and metalloproteinase domain-containing protein 10
D: Disintegrin and metalloproteinase domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,79823
Polymers198,2494
Non-polymers5,54819
Water6,900383
1
A: Disintegrin and metalloproteinase domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6755
Polymers49,5621
Non-polymers1,1124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Disintegrin and metalloproteinase domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0956
Polymers49,5621
Non-polymers1,5335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Disintegrin and metalloproteinase domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7716
Polymers49,5621
Non-polymers1,2085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Disintegrin and metalloproteinase domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2576
Polymers49,5621
Non-polymers1,6955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.420, 188.780, 86.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Disintegrin and metalloproteinase domain-containing protein 10 / ADAM 10 / CDw156 / Kuzbanian protein homolog / Mammalian disintegrin-metalloprotease


Mass: 49562.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAM10, KUZ, MADM / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O14672, ADAM10 endopeptidase

-
Sugars , 4 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 398 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.26M Ammonium Sulfate 100mM HEPES pH 7.5 21.75 % PEG8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→47.476 Å / Num. obs: 52456 / % possible obs: 97.37 % / Redundancy: 3.1 % / CC1/2: 0.959 / Net I/av σ(I): 4.8 / Net I/σ(I): 4.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.35 / Num. unique obs: 5184 / CC1/2: 0.323 / % possible all: 97.99

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BKC

1bkc


Resolution: 2.8→47.476 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2845 4849 5.04 %
Rwork0.2363 --
obs0.2387 52448 93.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→47.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13275 0 342 383 14000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414096
X-RAY DIFFRACTIONf_angle_d0.50619034
X-RAY DIFFRACTIONf_dihedral_angle_d19.0515488
X-RAY DIFFRACTIONf_chiral_restr0.0412045
X-RAY DIFFRACTIONf_plane_restr0.0032461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83180.42781430.37362748X-RAY DIFFRACTION87
2.8318-2.86510.39551800.34433189X-RAY DIFFRACTION96
2.8651-2.90010.37791690.3143158X-RAY DIFFRACTION98
2.9001-2.93680.31811690.3083171X-RAY DIFFRACTION98
2.9368-2.97540.37181710.323176X-RAY DIFFRACTION98
2.9754-3.01620.38961700.32673188X-RAY DIFFRACTION98
3.0162-3.05920.40171680.32043156X-RAY DIFFRACTION97
3.0592-3.10490.37441670.32443182X-RAY DIFFRACTION97
3.1049-3.15340.37561650.3163125X-RAY DIFFRACTION97
3.1534-3.20510.35381670.30533130X-RAY DIFFRACTION95
3.2051-3.26030.33641550.28473011X-RAY DIFFRACTION95
3.2603-3.31960.33731610.27653046X-RAY DIFFRACTION93
3.3196-3.38340.36621500.27482971X-RAY DIFFRACTION91
3.3834-3.45250.29821560.26342746X-RAY DIFFRACTION84
3.4525-3.52750.29471540.25352911X-RAY DIFFRACTION91
3.5275-3.60960.27361730.24953165X-RAY DIFFRACTION97
3.6096-3.69980.31951660.25163130X-RAY DIFFRACTION97
3.6998-3.79980.30991680.22623129X-RAY DIFFRACTION97
3.7998-3.91160.3091630.22393132X-RAY DIFFRACTION96
3.9116-4.03770.27261590.21113133X-RAY DIFFRACTION96
4.0377-4.1820.20531620.19433042X-RAY DIFFRACTION95
4.182-4.34930.28981560.18122998X-RAY DIFFRACTION91
4.3493-4.54710.22611390.16982720X-RAY DIFFRACTION84
4.5471-4.78660.20581630.17013001X-RAY DIFFRACTION93
4.7866-5.08620.21831660.17643115X-RAY DIFFRACTION96
5.0862-5.47840.25911590.19233103X-RAY DIFFRACTION96
5.4784-6.02870.24711600.18653048X-RAY DIFFRACTION94
6.0287-6.89880.18241470.1992763X-RAY DIFFRACTION85
6.8988-8.68310.19761640.1923088X-RAY DIFFRACTION95
8.6831-47.4830.23141590.20692961X-RAY DIFFRACTION91

+
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