[English] 日本語
Yorodumi
- PDB-5hhd: Crystal Structure of Chemically Synthesized Heterochiral {RFX037 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hhd
TitleCrystal Structure of Chemically Synthesized Heterochiral {RFX037 plus VEGF-A} Protein Complex in space group P21
Components
  • D-Peptide RFX037.D
  • D-Vascular endothelial growth factor
  • L-Peptide RFX037.L
  • Vascular endothelial growth factor A
KeywordsDE NOVO PROTEIN / HETEROCHIRAL PROTEIN-PROTEIN COMPLEX / D-PROTEIN ANTAGONIST / GROWTH FACTOR-INHIBITOR COMPLEX / RACEMIC CRYSTALLOGRAPHY
Function / homology
Function and homology information


Signaling by VEGF / basophil chemotaxis / lymph vessel morphogenesis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / : / VEGF ligand-receptor interactions / vascular endothelial growth factor receptor 1 binding / negative regulation of adherens junction organization / post-embryonic camera-type eye development ...Signaling by VEGF / basophil chemotaxis / lymph vessel morphogenesis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / : / VEGF ligand-receptor interactions / vascular endothelial growth factor receptor 1 binding / negative regulation of adherens junction organization / post-embryonic camera-type eye development / primitive erythrocyte differentiation / positive regulation of mast cell chemotaxis / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / negative regulation of blood-brain barrier permeability / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / VEGF-activated neuropilin signaling pathway / motor neuron migration / eye photoreceptor cell development / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / mammary gland alveolus development / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor receptor-2 signaling pathway / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of axon extension involved in axon guidance / camera-type eye morphogenesis / endothelial cell chemotaxis / positive regulation of protein localization to early endosome / positive regulation of trophoblast cell migration / surfactant homeostasis / retinal ganglion cell axon guidance / induction of positive chemotaxis / vascular wound healing / positive regulation of protein autophosphorylation / dopaminergic neuron differentiation / positive regulation of epithelial tube formation / neuropilin binding / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / tube formation / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of leukocyte migration / cell migration involved in sprouting angiogenesis / vascular endothelial growth factor receptor 2 binding / positive regulation of vascular permeability / commissural neuron axon guidance / artery morphogenesis / branching involved in blood vessel morphogenesis / cardiac muscle cell development / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of blood vessel branching / sprouting angiogenesis / platelet-derived growth factor receptor binding / extracellular matrix binding / positive regulation of positive chemotaxis / positive regulation of neuroblast proliferation / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of endothelial cell chemotaxis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of DNA biosynthetic process / negative regulation of epithelial to mesenchymal transition / vascular endothelial growth factor signaling pathway / positive chemotaxis / positive regulation of sprouting angiogenesis / mesoderm development / ovarian follicle development / chemoattractant activity / cell maturation / outflow tract morphogenesis / lung development / vasculogenesis / macrophage differentiation / fibronectin binding / monocyte differentiation / positive regulation of cell division / cellular response to vascular endothelial growth factor stimulus / heart morphogenesis / positive regulation of receptor internalization / positive regulation of focal adhesion assembly / vascular endothelial growth factor receptor signaling pathway / positive regulation of blood vessel endothelial cell migration / lactation / kidney development / positive regulation of endothelial cell proliferation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / epithelial cell differentiation / positive regulation of epithelial cell proliferation / in utero embryonic development / positive regulation of endothelial cell migration / negative regulation of miRNA transcription / positive regulation of cell adhesion / secretory granule / platelet alpha granule lumen / cytokine activity / VEGFR2 mediated cell proliferation / growth factor activity / adherens junction / positive regulation of protein-containing complex assembly
Similarity search - Function
Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / Vascular endothelial growth factor A, long form-like domain / : / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. ...Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / Vascular endothelial growth factor A, long form-like domain / : / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family / Ubiquitin-like (UB roll) - #10 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Ubiquitin-like (UB roll) / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / polypeptide(D) / polypeptide(D) (> 10) / polypeptide(D) (> 100) / Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsUppalapati, M. / LEE, D.J. / Mandal, K. / Kent, S.B.H. / Sidhu, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)RR-15301 United States
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: A Potent d-Protein Antagonist of VEGF-A is Nonimmunogenic, Metabolically Stable, and Longer-Circulating in Vivo.
Authors: Uppalapati, M. / Lee, D.J. / Mandal, K. / Li, H. / Miranda, L.P. / Lowitz, J. / Kenney, J. / Adams, J.J. / Ault-Riche, D. / Kent, S.B. / Sidhu, S.S.
History
DepositionJan 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vascular endothelial growth factor A
B: Vascular endothelial growth factor A
C: D-Peptide RFX037.D
D: D-Peptide RFX037.D
E: D-Vascular endothelial growth factor
F: D-Vascular endothelial growth factor
G: L-Peptide RFX037.L
H: L-Peptide RFX037.L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,49713
Polymers79,0238
Non-polymers4745
Water6,179343
1
A: Vascular endothelial growth factor A
B: Vascular endothelial growth factor A
C: D-Peptide RFX037.D
D: D-Peptide RFX037.D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7897
Polymers39,5124
Non-polymers2763
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-47 kcal/mol
Surface area17100 Å2
MethodPISA
2
E: D-Vascular endothelial growth factor
F: D-Vascular endothelial growth factor
G: L-Peptide RFX037.L
H: L-Peptide RFX037.L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7086
Polymers39,5104
Non-polymers1982
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-41 kcal/mol
Surface area16830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.290, 87.240, 81.344
Angle α, β, γ (deg.)90.00, 101.42, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 4 types, 8 molecules ABCDEFGH

#1: Protein Vascular endothelial growth factor A / VEGF-A / Vascular permeability factor / VPF


Mass: 11948.680 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical Synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: P15692
#2: Protein D-Peptide RFX037.D


Mass: 7807.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein D-Vascular endothelial growth factor


Mass: 11942.639 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Protein L-Peptide RFX037.L


Mass: 7812.501 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 348 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Proteins were dissolved in 0.01 M HEPES at pH 7.0 and crystallized against reservoir containing 0.1 M MgCl2, 0.1 M HEPES (pH 7.0), 11% (v/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 43802 / % possible obs: 99.2 % / Redundancy: 7.4 % / Biso Wilson estimate: 33.78 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 5.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.625 / % possible all: 92.9

-
Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HHC

5hhc


Resolution: 2.1→49.62 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.282 2203 5.06 %
Rwork0.222 --
obs0.225 43521 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.77 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5088 0 31 343 5462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085406
X-RAY DIFFRACTIONf_angle_d1.067279
X-RAY DIFFRACTIONf_dihedral_angle_d15.5961977
X-RAY DIFFRACTIONf_chiral_restr0.064779
X-RAY DIFFRACTIONf_plane_restr0.005954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0993-2.14490.36971220.30862274X-RAY DIFFRACTION87
2.1449-2.19480.38071340.29082574X-RAY DIFFRACTION98
2.1948-2.24970.33511340.25932548X-RAY DIFFRACTION98
2.2497-2.31050.2961290.2442595X-RAY DIFFRACTION99
2.3105-2.37850.34161600.23422570X-RAY DIFFRACTION99
2.3785-2.45530.30881500.23212547X-RAY DIFFRACTION99
2.4553-2.5430.33311380.23612620X-RAY DIFFRACTION99
2.543-2.64490.27771240.23482605X-RAY DIFFRACTION99
2.6449-2.76520.31861440.23962589X-RAY DIFFRACTION99
2.7652-2.9110.34881320.24142606X-RAY DIFFRACTION99
2.911-3.09340.34361200.24732616X-RAY DIFFRACTION99
3.0934-3.33210.28971350.23262620X-RAY DIFFRACTION99
3.3321-3.66740.26691460.22932628X-RAY DIFFRACTION99
3.6674-4.19780.2571210.19082635X-RAY DIFFRACTION100
4.1978-5.28790.22421660.17012620X-RAY DIFFRACTION100
5.2879-49.63550.24551480.22012671X-RAY DIFFRACTION99
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)
10.0102-0.00010.00740.00280.00420.0073-0.2526-0.0658-0.07350.1960.0039-0.029-0.22530.21020.00030.3531-0.0026-0.00130.3094-0.00970.3653-23.343110.9035-0.3536
20.0398-0.09790.02790.2208-0.10760.1256-0.0097-0.0329-0.09810.2005-0.02450.0332-0.0825-0.01830.00350.3248-0.2008-0.03650.4593-0.01530.287-16.983320.5624-22.7612
30.0144-0.05430.02950.0147-0.05930.0478-0.29990.2835-0.0123-0.1590.01610.0948-0.1055-0.0329-0.00010.3963-0.12330.00480.3897-0.01110.3495-23.412913.7122-20.2944
40.0841-0.07990.12550.2203-0.17210.2756-0.125-0.01680.0780.12560.23770.09660.0629-0.34520.23860.0923-0.21760.04650.0752-0.06380.2713-35.433711.0859-6.0303
50.0751-0.05130.05240.0361-0.03480.0378-0.06480.04860.0692-0.0308-0.03130.0125-0.0104-0.0001-0.07120.4069-0.3389-0.02720.3466-0.02720.3566-30.9686.7741-25.1474
60.0050.00260.01080.0108-0.00150.011-0.0284-0.0102-0.190.12020.0409-0.00080.1149-0.04760.00010.39270.0640.00650.4248-0.02950.2566-25.49767.873520.0655
70.0068-0.0165-0.00930.03670.03120.0181-0.08760.0577-0.0459-0.0194-0.0711-0.00980.1595-0.00550.00010.3576-0.05440.03130.24350.05140.3071-10.50968.79-48.5194
80.1278-0.1515-0.09620.2010.02010.0796-0.132-0.1755-0.0429-0.04170.1614-0.00440.2505-0.1373-0.00850.3515-0.0647-0.01710.3920.0340.3296-4.6648-16.4566-18.5313
90.1796-0.1716-0.01860.1673-0.04350.26320.2745-0.0729-0.2933-0.0126-0.2820.0879-0.09720.3150.00330.3101-0.0429-0.01080.45310.03120.355213.7857-5.8504-29.3088
100.00780.010.00370.00960.00510.0040.0305-0.0366-0.023-0.0280.09740.1383-0.0554-0.04250.00010.2762-0.08880.04960.38020.18960.38912.758-1.0923-56.9129
110.02590.015-0.01070.00850.00080.0064-0.05330.0466-0.0341-0.0794-0.0690.0103-0.12710.0924-00.3965-0.1024-0.04460.5750.04550.38918.2896-0.1028-62.5049
120.01810.01370.02740.011-0.00360.06360.21120.0997-0.042-0.0838-0.02050.06630.35350.2422-00.37910.0234-0.04160.3510.00350.29017.2871-5.4334-52.1705
130.1607-0.06990.0220.03060.00090.12780.0615-0.00350.01910.00260.05030.0518-0.0814-0.06830.00770.2820.24460.0160.67110.06770.3472-2.80021.5215-51.1057
140.0226-0.0113-0.00390.03850.01980.0307-0.08020.04740.1101-0.0812-0.0329-0.0481-0.1156-0.0114-0.00010.5423-0.10310.06570.5844-0.01940.402-9.7262-2.49957.7437
150.00920.0031-0.00090.002-0.00180.001-0.0329-0.042-0.0580.09410.05250.0798-0.0260.00060.00010.658-0.07890.05880.5497-0.13440.3755-7.51570.941610.4063
160.0211-0.0164-0.0120.05030.05460.04320.02530.04990.04260.22570.22720.03010.14390.0489-0.00010.51040.0581-0.12010.7285-0.03070.4671-4.4247-6.2322.1907
170.0032-0.00750.00340.0131-0.00990.00780.04380.03910.0033-0.0469-0.00270.0065-0.0436-0.00270.00050.6380.1479-0.01020.33760.01930.3351-6.28715.3598-1.6295
180.006-0.0003-0.00080.02520.01470.05040.1561-0.1114-0.05080.02170.12090.0247-0.002-0.04360.07780.3257-0.22730.00580.4508-0.04230.3522-18.169821.0905-18.3772
190.06350.0007-0.06580.0127-0.01480.06170.1256-0.0458-0.080.1520.0063-0.0265-0.05190.11640.10570.2673-0.2739-0.0140.46850.0120.3093-12.173624.0697-20.952
200.04390.0159-0.00790.01310.00880.02320.0955-0.25360.00950.1006-0.1443-0.1347-0.0372-0.019-0.01750.3415-0.4134-0.04750.5010.03860.4145-12.449324.1891-28.2533
210.0123-0.0042-0.00250.0339-0.02610.0151-0.25810.16350.0836-0.11190.04450.0128-0.0372-0.03760.00010.3366-0.0514-0.05540.2693-0.04030.3562-29.344613.7075-8.9506
220.0355-0.00280.06190.0149-0.02730.1204-0.1145-0.0061-0.090.02470.0541-0.0467-0.09170.1346-00.42510.0096-0.00350.2512-0.02980.3423-25.064111.447412.1404
23-0.0015-0.0036-0.00010.07610.090.0899-0.0184-0.08840.0154-0.0247-0.21260.12050.0660.083900.3925-0.10590.08080.27330.00090.3827-14.875411.4389-41.396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 10 THROUGH 19 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 39 THROUGH 52 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 10 THROUGH 31 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 59 THROUGH 92 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 93 THROUGH 96 )
6X-RAY DIFFRACTION6CHAIN 'C' AND (RESID 10 THROUGH 24 )
7X-RAY DIFFRACTION7CHAIN 'D' AND (RESID 10 THROUGH 24 )
8X-RAY DIFFRACTION8CHAIN 'E' AND (RESID 51 THROUGH 85 )
9X-RAY DIFFRACTION9CHAIN 'F' AND (RESID 51 THROUGH 85 )
10X-RAY DIFFRACTION10CHAIN 'G' AND (RESID 10 THROUGH 15 )
11X-RAY DIFFRACTION11CHAIN 'G' AND (RESID 16 THROUGH 24 )
12X-RAY DIFFRACTION12CHAIN 'G' AND (RESID 30 THROUGH 54 )
13X-RAY DIFFRACTION13CHAIN 'G' AND (RESID 55 THROUGH 60 )
14X-RAY DIFFRACTION14CHAIN 'H' AND (RESID 10 THROUGH 19 )
15X-RAY DIFFRACTION15CHAIN 'H' AND (RESID 20 THROUGH 24 )
16X-RAY DIFFRACTION16CHAIN 'H' AND (RESID 30 THROUGH 54 )
17X-RAY DIFFRACTION17CHAIN 'H' AND (RESID 55 THROUGH 60 )
18X-RAY DIFFRACTION18CHAIN 'A' AND (RESID 20 THROUGH 31 )
19X-RAY DIFFRACTION19CHAIN 'A' AND (RESID 59 THROUGH 77 )
20X-RAY DIFFRACTION20CHAIN 'A' AND (RESID 78 THROUGH 96 )
21X-RAY DIFFRACTION21CHAIN 'B' AND (RESID 40 THROUGH 52 )
22X-RAY DIFFRACTION22CHAIN 'C' AND (RESID 30 THROUGH 60 )
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESID 30 THROUGH 60 )

+
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