[English] 日本語
Yorodumi
- PDB-6rur: Structure of the SCIN stabilized C3bBb convertase bound to properdin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rur
TitleStructure of the SCIN stabilized C3bBb convertase bound to properdin
Components
  • (Complement C3) x 2
  • (Properdin) x 2
  • Complement factor B
  • Inhibitor
KeywordsIMMUNE SYSTEM / innate immunity / complement / protease
Function / homology
Function and homology information


cytoplasmic side of Golgi membrane / alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex ...cytoplasmic side of Golgi membrane / alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement binding / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of lipid storage / positive regulation of phagocytosis, engulfment / complement receptor mediated signaling pathway / Activation of C3 and C5 / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / Peptide ligand-binding receptors / fatty acid metabolic process / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / specific granule lumen / positive regulation of angiogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / positive regulation of immune response / tertiary granule lumen / G alpha (i) signalling events / secretory granule lumen / blood microparticle / defense response to bacterium / inflammatory response / positive regulation of protein phosphorylation / immune response / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Staphylococcal complement inhibitor SCIN / Staphylococcal complement inhibitor SCIN / : / Thrombospondin type 1 repeat / Complement factor B / Complement B/C2 / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment ...Staphylococcal complement inhibitor SCIN / Staphylococcal complement inhibitor SCIN / : / Thrombospondin type 1 repeat / Complement factor B / Complement B/C2 / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Heat shock protein 70kD, C-terminal domain superfamily / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / von Willebrand factor type A domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan / Immunoglobulin-like fold
Similarity search - Domain/homology
alpha-D-mannopyranose / Staphylococcal complement inhibitor / Complement factor B / Complement C3 / Properdin / Staphylococcal complement inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6 Å
AuthorsPedersen, D.V. / Gadeberg, T.A.F. / Andersen, G.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
LundbeckfondenR155-2015-2666 Denmark
Citation
Journal: Front Immunol / Year: 2019
Title: Structural Basis for Properdin Oligomerization and Convertase Stimulation in the Human Complement System.
Authors: Pedersen, D.V. / Gadeberg, T.A.F. / Thomas, C. / Wang, Y. / Joram, N. / Jensen, R.K. / Mazarakis, S.M.M. / Revel, M. / El Sissy, C. / Petersen, S.V. / Lindorff-Larsen, K. / Thiel, S. / ...Authors: Pedersen, D.V. / Gadeberg, T.A.F. / Thomas, C. / Wang, Y. / Joram, N. / Jensen, R.K. / Mazarakis, S.M.M. / Revel, M. / El Sissy, C. / Petersen, S.V. / Lindorff-Larsen, K. / Thiel, S. / Laursen, N.S. / Fremeaux-Bacchi, V. / Andersen, G.R.
#1: Journal: Febs Lett. / Year: 2019
Title: Crystal structure of peptide-bound neprilysin reveals key binding interactions.
Authors: Moss, S. / Subramanian, V. / Acharya, K.R.
#2: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2019
Title: Crystallization and X-ray analysis of monodisperse human properdin.
Authors: Pedersen, D.V. / Revel, M. / Gadeberg, T.A.F. / Andersen, G.R.
History
DepositionMay 29, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionAug 21, 2019ID: 5M6W
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: chem_comp / citation / citation_author / Item: _chem_comp.type
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / pdbx_validate_close_contact / refine / 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 / _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.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.name / _chem_comp.type / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _refine.pdbx_diffrn_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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
U: Properdin
V: Properdin
X: Properdin
Y: Properdin
A: Complement C3
B: Complement C3
G: Complement C3
H: Complement C3
J: Complement factor B
L: Complement factor B
N: Inhibitor
Q: Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)592,63646
Polymers583,50312
Non-polymers9,13334
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53930 Å2
ΔGint-114 kcal/mol
Surface area233230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)634.870, 121.980, 264.420
Angle α, β, γ (deg.)90.00, 112.91, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

-
Protein , 6 types, 12 molecules UXVYAGBHJLNQ

#1: Protein Properdin / Complement factor P


Mass: 25494.734 Da / Num. of mol.: 2 / Mutation: TSR2 and TSR3 are not modelled
Source method: isolated from a genetically manipulated source
Details: TSR2 and TSR3 are not modelled and are therefore missing residues.
Source: (gene. exp.) Homo sapiens (human) / Gene: CFP, PFC / Production host: Homo sapiens (human) / Variant (production host): HEK293F / References: UniProt: P27918
#2: Protein Properdin / Complement factor P


Mass: 23929.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: properdin TSR4-TSR5-TSR6 fragment with a few additional residues from expression vector
Source: (gene. exp.) Homo sapiens (human) / Gene: CFP, PFC / Production host: Homo sapiens (human) / Variant (production host): HEK293F / References: UniProt: P27918
#3: Protein Complement C3 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1


Mass: 71393.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: complement C3 beta-chain / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#4: Protein Complement C3 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1


Mass: 104073.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: complement C3 alpha-prime chain / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#5: Protein Complement factor B / C3/C5 convertase / Glycine-rich beta glycoprotein / GBG / PBF2 / Properdin factor B


Mass: 57042.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFB, BF, BFD / Production host: Homo sapiens (human)
References: UniProt: P00751, alternative-complement-pathway C3/C5 convertase
#6: Protein Inhibitor / Involved in expression of fibrinogen binding protein / phage associated / Staphylococcal complement inhibitor


Mass: 9819.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: scn_3, scn, scn_2, scn_4, BN1321_320035, CV021_13080, D1G05_09530, D1G09_13565, D1G21_11725, EP54_10460, EQ90_13920, ERS072840_02186, NCTC10654_02112, NCTC10702_03129, NCTC13196_02025, ...Gene: scn_3, scn, scn_2, scn_4, BN1321_320035, CV021_13080, D1G05_09530, D1G09_13565, D1G21_11725, EP54_10460, EQ90_13920, ERS072840_02186, NCTC10654_02112, NCTC10702_03129, NCTC13196_02025, NCTC13196_03045, NCTC6133_02657, NCTC7878_02651
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2DUF0, UniProt: Q931M7*PLUS

-
Sugars , 4 types, 32 molecules

#7: Polysaccharide
beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3LFucpa1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1221m-1a_1-5][a2122h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-L-Fucp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#8: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#9: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#10: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 1 types, 2 molecules

#11: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Mg

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 50 mM MgAcetate 50 mM Mes 6.5 5 % w/v PEG 10K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 6→48.76 Å / Num. obs: 47262 / % possible obs: 99.5 % / Redundancy: 6.249 % / Biso Wilson estimate: 301.82 Å2 / Net I/σ(I): 5.17
Reflection shellResolution: 6→6.27 Å / Num. unique obs: 5785 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WIN

2win


Resolution: 6→48.764 Å / SU ML: 1.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2721 1174 2.51 %
Rwork0.2336 --
obs0.2345 46730 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 6→48.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38872 0 584 0 39456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00240395
X-RAY DIFFRACTIONf_angle_d0.56554878
X-RAY DIFFRACTIONf_dihedral_angle_d15.62224796
X-RAY DIFFRACTIONf_chiral_restr0.0436176
X-RAY DIFFRACTIONf_plane_restr0.0046998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6-6.27260.39061560.36335629X-RAY DIFFRACTION99
6.2726-6.60250.37111360.35025717X-RAY DIFFRACTION99
6.6025-7.01510.37891470.33095674X-RAY DIFFRACTION99
7.0151-7.55490.35031540.29855699X-RAY DIFFRACTION99
7.5549-8.31180.27751350.25075655X-RAY DIFFRACTION99
8.3118-9.50680.21531490.18515679X-RAY DIFFRACTION98
9.5068-11.94840.21151470.17325711X-RAY DIFFRACTION98
11.9484-48.76540.27021500.22275792X-RAY DIFFRACTION97

+
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://pdbjlvh1.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