[English] 日本語
Yorodumi
- PDB-2w6t: Structures of P. aeruginosa FpvA bound to heterologous pyoverdine... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2w6t
TitleStructures of P. aeruginosa FpvA bound to heterologous pyoverdines: FpvA-Pvd(DSM50106)-Fe complex
Components
  • FERRIPYOVERDINE RECEPTOR
  • PYOVERDINE
KeywordsMEMBRANE PROTEIN / RECEPTOR / TONB BOX / TRANSPORT / SIDEROPHORE / CELL MEMBRANE / ION TRANSPORT / IRON TRANSPORT / OUTER MEMBRANE / TONB-DEPENDENT TRANSPORTER
Function / homology
Function and homology information


pyoverdine biosynthetic process / siderophore uptake transmembrane transporter activity / cell outer membrane / signaling receptor activity / membrane
Similarity search - Function
Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent siderophore receptor ...Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / 3-Layer(bab) Sandwich / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Synthetic PYOVERDINE Fe Complex / : / PHOSPHATE ION / Chem-PVE / Ferripyoverdine receptor
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
PSEUDOMONAS FLUORESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGreenwald, J. / Nader, M. / Celia, H. / Gruffaz, C. / Meyer, J.-M. / Schalk, I.J. / Pattus, F.
CitationJournal: Mol.Microbiol. / Year: 2009
Title: Fpva Bound to Non-Cognate Pyoverdines: Molecular Basis of Siderophore Recognition by an Iron Transporter.
Authors: Greenwald, J. / Nader, M. / Celia, H. / Gruffaz, C. / Geoffroy, V. / Meyer, J.M. / Schalk, I.J. / Pattus, F.
History
DepositionDec 19, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Mar 19, 2014Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Structure summary
Revision 1.4Dec 28, 2016Group: Source and taxonomy / Structure summary
Revision 1.5Jul 24, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 22-STRANDED BARREL THIS IS REPRESENTED BY A 23-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FERRIPYOVERDINE RECEPTOR
B: FERRIPYOVERDINE RECEPTOR
C: PYOVERDINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,23517
Polymers174,1523
Non-polymers2,08314
Water00
1
A: FERRIPYOVERDINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8279
Polymers86,5561
Non-polymers1,2718
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FERRIPYOVERDINE RECEPTOR
C: PYOVERDINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4088
Polymers87,5962
Non-polymers8126
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-9.3 kcal/mol
Surface area40200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.557, 129.126, 141.817
Angle α, β, γ (deg.)90.00, 131.65, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein FERRIPYOVERDINE RECEPTOR / FPVA


Mass: 86556.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PPVR2 / Production host: PSEUDOMONAS AERUGINOSA (bacteria) / Strain (production host): K691 / References: UniProt: P48632
#2: Protein/peptide PYOVERDINE / DSN-LYS-GLY-FHO-SER-DSN-GLY-ORN-FHO-SER


Type: Polypeptide / Class: Metal transport / Mass: 1040.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: IN IRON-DEFICIENT CONDITIONS, PSEUDOMONAS AERUGINOSA SECRETES A MAJOR FLUORESCENT SIDEROPHORE NAMED PYOVERDIN (PVD), WHICH AFTER CHELATING IRON(III) IS TRANSPORTED BACK INTO THE CELL VIA ITS ...Details: IN IRON-DEFICIENT CONDITIONS, PSEUDOMONAS AERUGINOSA SECRETES A MAJOR FLUORESCENT SIDEROPHORE NAMED PYOVERDIN (PVD), WHICH AFTER CHELATING IRON(III) IS TRANSPORTED BACK INTO THE CELL VIA ITS OUTER MEMBRANE RECEPTOR FPVA. FPVA IS A TONB-DEPENDENT TRANSPORT PROTEIN AND HAS THE ABILITY TO BIND PVD IN ITS APO- OR IRON-LOADED FORM.
Source: (natural) PSEUDOMONAS FLUORESCENS (bacteria) / References: Synthetic PYOVERDINE Fe Complex

-
Non-polymers , 4 types, 14 molecules

#3: Chemical ChemComp-N8E / 3,6,9,12,15-PENTAOXATRICOSAN-1-OL / N-OCTYLPENTAOXYETHYLENE / PENTAETHYLENE GLYCOL MONOOCTYL ETHER / OCTYLPENTAGLYCOL N-OCTYLPENTAOXYETHYLENE


Mass: 350.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O6 / Comment: C8E5, detergent*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PVE / (1S)-1-CARBOXY-5-[(3-CARBOXYPROPANOYL)AMINO]-8,9-DIHYDROXY-1,2,3,4-TETRAHYDROPYRIMIDO[1,2-A]QUINOLIN-11-IUM


Type: Polypeptide / Class: Metal transport / Mass: 376.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N3O7
Details: IN IRON-DEFICIENT CONDITIONS, PSEUDOMONAS AERUGINOSA SECRETES A MAJOR FLUORESCENT SIDEROPHORE NAMED PYOVERDIN (PVD), WHICH AFTER CHELATING IRON(III) IS TRANSPORTED BACK INTO THE CELL VIA ITS ...Details: IN IRON-DEFICIENT CONDITIONS, PSEUDOMONAS AERUGINOSA SECRETES A MAJOR FLUORESCENT SIDEROPHORE NAMED PYOVERDIN (PVD), WHICH AFTER CHELATING IRON(III) IS TRANSPORTED BACK INTO THE CELL VIA ITS OUTER MEMBRANE RECEPTOR FPVA. FPVA IS A TONB-DEPENDENT TRANSPORT PROTEIN AND HAS THE ABILITY TO BIND PVD IN ITS APO- OR IRON-LOADED FORM.
References: Synthetic PYOVERDINE Fe Complex
#6: Chemical ChemComp-FE / FE (III) ION


Type: Polypeptide / Class: Metal transport / Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
Details: IN IRON-DEFICIENT CONDITIONS, PSEUDOMONAS AERUGINOSA SECRETES A MAJOR FLUORESCENT SIDEROPHORE NAMED PYOVERDIN (PVD), WHICH AFTER CHELATING IRON(III) IS TRANSPORTED BACK INTO THE CELL VIA ITS ...Details: IN IRON-DEFICIENT CONDITIONS, PSEUDOMONAS AERUGINOSA SECRETES A MAJOR FLUORESCENT SIDEROPHORE NAMED PYOVERDIN (PVD), WHICH AFTER CHELATING IRON(III) IS TRANSPORTED BACK INTO THE CELL VIA ITS OUTER MEMBRANE RECEPTOR FPVA. FPVA IS A TONB-DEPENDENT TRANSPORT PROTEIN AND HAS THE ABILITY TO BIND PVD IN ITS APO- OR IRON-LOADED FORM.
References: Synthetic PYOVERDINE Fe Complex

-
Details

Compound detailsPYOVERDINES ARE A GROUP OF STRUCTURALLY RELATED SIDEROPHORES PRODUCED BY FLUORESCENT PSEUDOMONAS ...PYOVERDINES ARE A GROUP OF STRUCTURALLY RELATED SIDEROPHORES PRODUCED BY FLUORESCENT PSEUDOMONAS SPECIES. PYOVERDINE IS NECESSARY FOR INFECTION IN SEVERAL DIFFERENT DISEASE MODELS. THE OCCURRENCE OF PYOVERDINE-DEFECTIVE STRAINS IN CHRONIC INFECTIONS OF PATIENTS WITH CYSTIC FIBROSIS AND THE EXTREMELY HIGH SEQUENCE DIVERSITY OF GENES INVOLVED IN PYOVERDINE SYNTHESIS AND UPTAKE INDICATE THAT PYOVERDINE PRODUCTION IS SUBJECT TO HIGH EVOLUTIONARY PRESSURE. PYOVERDINE-DEPENDENT IRON TRANSPORT IS ALSO CRUCIAL FOR BIOFILM DEVELOPMENT, FURTHER EXPANDING THE IMPORTANCE OF THESE SIDEROPHORES IN PSEUDOMONAS BIOLOGY. GROUP: 1 NAME: FERRIPYOVERDINE FPVA-PVD(G173)-FE COMPLEX CHAIN: C COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 3 TO 12 COMPONENT_2: PYOVERDINE-CHROMOPHORE RESIDUE PVE 1 COMPONENT_3: FE (III) ION RESIDUE FE 2 DESCRIPTION: IN IRON-DEFICIENT CONDITIONS, PSEUDOMONAS AERUGINOSA SECRETES A MAJOR FLUORESCENT SIDEROPHORE NAMED PYOVERDIN (PVD), WHICH AFTER CHELATING IRON(III) IS TRANSPORTED BACK INTO THE CELL VIA ITS OUTER MEMBRANE RECEPTOR FPVA. FPVA IS A TONB-DEPENDENT TRANSPORT PROTEIN AND HAS THE ABILITY TO BIND PVD IN ITS APO- OR IRON-LOADED FORM.
Nonpolymer detailsC8E5 (N8E): DETERGENT
Sequence detailsSIGNAL PEPTIDE (RESIDUES 1-43) IS NOT IN THE CRYSTALLIZED PROTEIN.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 67.82 % / Description: NONE
Crystal growDetails: 1.3M NAH2PO4, 0.1M MES, PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 2.9→107 Å / Num. obs: 54303 / % possible obs: 93.7 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.6
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.3 / % possible all: 94.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O5P

2o5p


Resolution: 2.9→106 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.853 / SU B: 30.04 / SU ML: 0.266 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 1.478 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2785 5.1 %RANDOM
Rwork0.205 ---
obs0.208 51513 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.71 Å2
Baniso -1Baniso -2Baniso -3
1-2.24 Å20 Å22.85 Å2
2---0.12 Å20 Å2
3---1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.9→106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12179 0 125 0 12304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02212639
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9811.94517142
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2151534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07724.257639
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.765151972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8291578
X-RAY DIFFRACTIONr_chiral_restr0.1330.21772
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029859
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.25010
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.28276
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2451
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.81.57789
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.318212222
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.19435699
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4214.54920
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
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.367 202
Rwork0.254 3798
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)
12.8936-0.29041.19828.4114-1.90528.06650.29220.091-0.1884-0.1317-0.3130.14580.60290.27910.0209-0.18520.06060.0688-0.12050.0457-0.1491-10.706-31.81353.541
20.75080.1682-0.29491.0482-0.37491.23340.0077-0.03620.06030.00510.0583-0.0289-0.08960.0604-0.0661-0.1574-0.0330.0574-0.1557-0.0402-0.1388-5.059-0.96134.703
311.04451.6845-2.971110.3763-0.67299.4738-0.1711-0.54050.08720.10470.11130.4323-0.02330.13240.0598-0.0910.05040.06290.0190.09220.0129-29.9134.465-10.031
41.42240.528-0.29151.2452-0.25191.0145-0.06190.17830.1572-0.1463-0.00920.0844-0.0126-0.1320.071-0.0975-0.03360.0027-0.10660.0152-0.0213-60.333-20.68714.365
59.392-0.53993.39390.11850.42335.59740.25210.0113-0.2062-0.2163-0.180.09970.33580.0975-0.0720.115-0.0854-0.01140.16120.00980.102-67.296-38.23221.393
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 129
2X-RAY DIFFRACTION2A130 - 815
3X-RAY DIFFRACTION3B44 - 117
4X-RAY DIFFRACTION4B136 - 815
5X-RAY DIFFRACTION5C1 - 12

+
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