[English] 日本語
Yorodumi
- PDB-4cak: Three-dimensional reconstruction of intact human integrin alphaII... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cak
TitleThree-dimensional reconstruction of intact human integrin alphaIIbbeta3 in a phospholipid bilayer nanodisc
Components
  • Integrin alpha-IIb
  • Integrin beta-3
KeywordsCELL ADHESION / INTEGRIN / SINGLE PARTICLE RECONSTRUCTION
Function / homology
Function and homology information


regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / alpha9-beta1 integrin-ADAM8 complex / response to platelet-derived growth factor / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / platelet alpha granule membrane ...regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / alpha9-beta1 integrin-ADAM8 complex / response to platelet-derived growth factor / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / smooth muscle cell migration / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / positive regulation of leukocyte migration / alphav-beta3 integrin-HMGB1 complex / negative regulation of lipid transport / vascular endothelial growth factor receptor 2 binding / angiogenesis involved in wound healing / positive regulation of vascular endothelial growth factor signaling pathway / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / positive regulation of bone resorption / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / cell-cell adhesion mediated by integrin / filopodium membrane / extracellular matrix binding / glycinergic synapse / positive regulation of fibroblast migration / positive regulation of cell adhesion mediated by integrin / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / negative regulation of low-density lipoprotein particle clearance / apoptotic cell clearance / wound healing, spreading of epidermal cells / positive regulation of smooth muscle cell migration / integrin complex / Molecules associated with elastic fibres / heterotypic cell-cell adhesion / cell adhesion mediated by integrin / negative chemotaxis / positive regulation of osteoblast proliferation / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / cellular response to insulin-like growth factor stimulus / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / regulation of postsynaptic neurotransmitter receptor internalization / cell-substrate adhesion / protein disulfide isomerase activity / microvillus membrane / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of endothelial cell apoptotic process / TGF-beta receptor signaling activates SMADs / lamellipodium membrane / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / Integrin cell surface interactions / ECM proteoglycans / substrate adhesion-dependent cell spreading / positive regulation of T cell migration / cell-matrix adhesion / embryo implantation / coreceptor activity / Integrin signaling / positive regulation of endothelial cell proliferation / positive regulation of smooth muscle cell proliferation / positive regulation of endothelial cell migration / cell adhesion molecule binding / integrin-mediated signaling pathway / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / response to activity / protein kinase C binding / wound healing / Signal transduction by L1 / cellular response to xenobiotic stimulus / regulation of actin cytoskeleton organization / cell-cell adhesion / cellular response to mechanical stimulus / platelet activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / platelet aggregation / VEGFA-VEGFR2 Pathway / integrin binding / ruffle membrane / blood coagulation / positive regulation of angiogenesis / Signaling by RAF1 mutants / cell-cell junction / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants
Similarity search - Function
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / : / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin alpha Ig-like domain 3 / Integrin_b_cyt / : / Integrin EGF domain ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / : / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin alpha Ig-like domain 3 / Integrin_b_cyt / : / Integrin EGF domain / EGF-like domain, extracellular / EGF-like domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin alpha cytoplasmic region / : / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / EGF-like domain signature 1. / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2.
Similarity search - Domain/homology
Integrin beta-3 / Integrin alpha-IIb
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 20.5 Å
AuthorsChoi, W.S. / Rice, W.J. / Stokes, D.L. / Coller, B.S.
CitationJournal: Blood / Year: 2013
Title: Three-dimensional reconstruction of intact human integrin αIIbβ3: new implications for activation-dependent ligand binding.
Authors: Won-Seok Choi / William J Rice / David L Stokes / Barry S Coller /
Abstract: Integrin αIIbβ3 plays a central role in hemostasis and thrombosis. We provide the first 3-dimensional reconstruction of intact purified αIIbβ3 in a nanodisc lipid bilayer. Unlike previous models, ...Integrin αIIbβ3 plays a central role in hemostasis and thrombosis. We provide the first 3-dimensional reconstruction of intact purified αIIbβ3 in a nanodisc lipid bilayer. Unlike previous models, it shows that the ligand-binding head domain is on top, pointing away from the membrane. Moreover, unlike the crystal structure of the recombinant ectodomain, the lower legs are not parallel, straight, and adjacent. Rather, the αIIb lower leg is bent between the calf-1 and calf-2 domains and the β3 Integrin-Epidermal Growth Factor (I-EGF) 2 to 4 domains are freely coiled rather than in a cleft between the β3 headpiece and the αIIb lower leg. Our data indicate an important role for the region that links the distal calf-2 and β-tail domains to their respective transmembrane (TM) domains in transmitting the conformational changes in the TM domains associated with inside-out activation.
History
DepositionOct 8, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Atomic model
Revision 1.2Jan 8, 2014Group: Database references
Revision 2.0Aug 23, 2017Group: Atomic model / Data collection / Refinement description
Category: atom_site / em_3d_fitting / em_software
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_alt_id / _atom_site.label_atom_id / _em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id
Revision 2.1Sep 11, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: database_PDB_caveat / entity ...database_PDB_caveat / entity / entity_name_com / entity_src_nat / struct_conn / struct_ref
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_nat.common_name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_organism_scientific / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_validate_close_contact / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Apr 9, 2025Group: 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 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_conn.pdbx_leaving_atom_flag
Revision 4.0Oct 1, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_modification_feature ...atom_site / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num ..._atom_site.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_2

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-2281
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrin alpha-IIb
B: Integrin beta-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,3159
Polymers180,7782
Non-polymers3,5377
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Integrin alpha-IIb / GPalpha IIb / GPIIb / Platelet membrane glycoprotein IIb


Mass: 104460.719 Da / Num. of mol.: 1 / Fragment: ECTODOMAIN, UNP RESIDUES 32-990 / Source method: isolated from a natural source / Details: FITTED FROM PDB ID 3FCS / Source: (natural) Homo sapiens (human) / Tissue: BLOOD / References: UniProt: P08514
#2: Protein Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 76316.945 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-716 / Source method: isolated from a natural source / Details: FITTED FROM PDB ID 3FCS / Source: (natural) Homo sapiens (human) / Cell line: PLATELET / Tissue: BLOOD / References: UniProt: P05106

-
Sugars , 5 types, 7 molecules

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


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-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
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: INTEGRIN ALPHAIIBBETA3 IN LIPID BILAYER NANODISC / Type: COMPLEX / Details: MICROGRAPHS TAKEN ON CCD
Buffer solutionName: 150 MM NACL, 10 MM HEPES, PH 7.4, 1 MM CACL2 AND 1 MM MGCL2
pH: 7.4
Details: 150 MM NACL, 10 MM HEPES, PH 7.4, 1 MM CACL2 AND 1 MM MGCL2
SpecimenConc.: 0.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: uranyl acetate
Specimen supportDetails: CARBON
VitrificationDetails: VITRIFICATION 1 -- CRYOGEN- NONE, INSTRUMENT- NONE,

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Feb 1, 2010
Details: LOW DOSE PACKAGE USED. CCD MAGNIFICATION IS 1.76 TIMES FILM MAGNIFICATION
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 29000 X / Calibrated magnification: 50592 X / Nominal defocus max: 1500 nm / Nominal defocus min: 1200 nm / Cs: 2 mm
Specimen holderTilt angle max: 50 ° / Tilt angle min: 0 °
Image recordingElectron dose: 13 e/Å2 / Film or detector model: GENERIC TVIPS (4k x 4k)
Image scansNum. digital images: 1500
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2SPIDER3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: RANDOM CONICAL TILT THEN REFERENCE BASED RECONSTRUCTION
Resolution: 20.5 Å / Num. of particles: 25008 / Nominal pixel size: 2.96 Å / Actual pixel size: 2.96 Å / Magnification calibration: 23A LAYERLINE OF TMV
Details: INITIAL MODEL FROM RANDOM CONICAL TILT FOLLOWED BY REFERENCE BASED REFINEMENT PDB FILE 3FCS WAS SPLIT INTO 20 SUBDOMAINS. THESE SUBDOMAINS WERE MANUALLY FITTED INTO THE EM VOLUME SUBMISSION ...Details: INITIAL MODEL FROM RANDOM CONICAL TILT FOLLOWED BY REFERENCE BASED REFINEMENT PDB FILE 3FCS WAS SPLIT INTO 20 SUBDOMAINS. THESE SUBDOMAINS WERE MANUALLY FITTED INTO THE EM VOLUME SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2281. (DEPOSITION ID: 11378).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 3FCS

3fcs


Accession code: 3FCS / Source name: PDB / Type: experimental model
RefinementHighest resolution: 20.5 Å
Refinement stepCycle: LAST / Highest resolution: 20.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12173 0 234 0 12407

+
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