[English] 日本語
Yorodumi
- PDB-6qp7: Drosophila Semaphorin 2a -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qp7
TitleDrosophila Semaphorin 2a
ComponentsSemaphorin-2A
KeywordsSIGNALING PROTEIN / axon guidance cue / developmental protein / cell signalling / semaphorin / signalling protein
Function / homology
Function and homology information


flight behavior / olfactory bulb axon guidance / Sema3A PAK dependent Axon repulsion / CRMPs in Sema3A signaling / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / synaptic target inhibition / dendrite guidance / Sema4D induced cell migration and growth-cone collapse / Other semaphorin interactions / sensory neuron axon guidance ...flight behavior / olfactory bulb axon guidance / Sema3A PAK dependent Axon repulsion / CRMPs in Sema3A signaling / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / synaptic target inhibition / dendrite guidance / Sema4D induced cell migration and growth-cone collapse / Other semaphorin interactions / sensory neuron axon guidance / semaphorin receptor binding / visual behavior / drinking behavior / chemorepellent activity / negative chemotaxis / adult behavior / semaphorin-plexin signaling pathway / endomembrane system / axon guidance / positive regulation of cell migration / extracellular region / plasma membrane / cytosol
Similarity search - Function
Semaphorin / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulin subtype ...Semaphorin / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsRobinson, R.A. / Rozbesky, D. / Harlos, K. / Siebold, C. / Jones, E.Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC375/A17721 United Kingdom
Medical Research Council (United Kingdom)MR/M000141/1 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Diversity of oligomerization in Drosophila semaphorins suggests a mechanism of functional fine-tuning.
Authors: Rozbesky, D. / Robinson, R.A. / Jain, V. / Renner, M. / Malinauskas, T. / Harlos, K. / Siebold, C. / Jones, E.Y.
History
DepositionFeb 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Semaphorin-2A
B: Semaphorin-2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,49935
Polymers150,7362
Non-polymers8,76433
Water14,286793
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18610 Å2
ΔGint147 kcal/mol
Surface area53290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.804, 109.977, 134.793
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Semaphorin-2A / Semaphorin-II / Sema II


Mass: 75367.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sema2a, Sema-2a, CG4700 / Cell line (production host): HEK293S-GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q24323

-
Sugars , 6 types, 11 molecules

#2: 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.: 4
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
#3: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[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: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[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: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1_g2-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+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-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+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

-
Non-polymers , 3 types, 815 molecules

#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 793 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris (pH 6.5) and 20% (w/v) PEG 5000 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.96→57.464 Å / Num. obs: 110704 / % possible obs: 99.6 % / Redundancy: 14.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.175 / Net I/σ(I): 11.51
Reflection shellResolution: 1.96→1.9823 Å

-
Processing

Software
NameVersionClassification
PHENIX(dev_3386: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OLZ

1olz


Resolution: 1.96→57.464 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.07
RfactorNum. reflection% reflection
Rfree0.2178 5611 5.07 %
Rwork0.1829 --
obs0.1847 110627 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.96→57.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10004 0 576 793 11373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310789
X-RAY DIFFRACTIONf_angle_d0.61314587
X-RAY DIFFRACTIONf_dihedral_angle_d12.5156508
X-RAY DIFFRACTIONf_chiral_restr0.0461673
X-RAY DIFFRACTIONf_plane_restr0.0031828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.98230.37911730.34733383X-RAY DIFFRACTION97
1.9823-2.00560.34061840.30253423X-RAY DIFFRACTION99
2.0056-2.03010.34272040.30313431X-RAY DIFFRACTION100
2.0301-2.05580.30131840.27183425X-RAY DIFFRACTION99
2.0558-2.08280.28142170.25663427X-RAY DIFFRACTION99
2.0828-2.11130.28982120.24063451X-RAY DIFFRACTION100
2.1113-2.14150.28541690.23753459X-RAY DIFFRACTION100
2.1415-2.17350.28551840.22883520X-RAY DIFFRACTION99
2.1735-2.20740.2411850.22133457X-RAY DIFFRACTION99
2.2074-2.24360.28421680.2163461X-RAY DIFFRACTION100
2.2436-2.28230.24732000.21983465X-RAY DIFFRACTION100
2.2823-2.32380.27371830.20653494X-RAY DIFFRACTION100
2.3238-2.36850.24291950.21133463X-RAY DIFFRACTION100
2.3685-2.41690.27991970.2113464X-RAY DIFFRACTION100
2.4169-2.46940.25791830.19963508X-RAY DIFFRACTION100
2.4694-2.52690.2541930.20583470X-RAY DIFFRACTION100
2.5269-2.59010.22031740.1953486X-RAY DIFFRACTION100
2.5901-2.66010.23381690.18863532X-RAY DIFFRACTION100
2.6601-2.73840.24121730.1863517X-RAY DIFFRACTION100
2.7384-2.82670.2171750.18413498X-RAY DIFFRACTION100
2.8267-2.92780.20181970.18293500X-RAY DIFFRACTION100
2.9278-3.0450.22821930.18063514X-RAY DIFFRACTION100
3.045-3.18360.21981810.17663522X-RAY DIFFRACTION100
3.1836-3.35140.18641990.16593545X-RAY DIFFRACTION100
3.3514-3.56130.20571690.15863553X-RAY DIFFRACTION100
3.5613-3.83630.19931760.15463541X-RAY DIFFRACTION100
3.8363-4.22220.17212030.14553563X-RAY DIFFRACTION100
4.2222-4.83290.1411770.13443589X-RAY DIFFRACTION100
4.8329-6.08790.18632010.16083613X-RAY DIFFRACTION100
6.0879-57.48910.21481930.18773742X-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)
19.0994-0.6829-4.17070.42530.80492.5651-1.15160.8917-0.3347-0.61060.55440.12320.5111-0.50690.58871.2105-0.1777-0.07670.94030.11930.8551-0.7296-9.8452-31.5253
20.940.0495-0.10660.65140.12821.0825-0.0103-0.0601-0.09510.00570.03390.01670.0026-0.0633-0.01940.15430.0135-0.00940.1690.03650.1939-16.3418-24.54360.352
36.29352.4989-0.94668.53111.03468.1938-0.260.58630.0721-0.32730.21280.08670.07080.07680.06540.15540.0020.00010.24250.05780.230310.6935-17.2874-23.3056
43.1192-0.7651-0.16016.3353-3.46816.36080.19160.02310.39590.0855-0.0657-0.1051-0.35570.0735-0.16830.38490.0177-0.00190.20870.04770.361110.50653.9147-32.528
53.57134.70363.79996.23445.03134.05680.6377-0.97380.1820.7982-0.3476-0.51170.26530.15-0.28750.7678-0.04730.06520.9284-0.00560.53951.023525.2939-21.1239
60.91990.3191-0.24231.07290.07382.59720.0394-0.08210.1219-0.08080.0204-0.0504-0.5120.3119-0.02830.2722-0.06970.04310.2449-0.03820.2264-6.328324.203815.0988
73.7051.81721.11327.29340.23196.6735-0.16090.3240.2391-0.03420.1968-0.0174-1.0368-0.269-0.06870.44830.05950.05880.30510.03290.254-13.333231.3922-19.8491
83.5095-0.84930.17386.99941.26394.7730.06970.6221-0.4767-0.2971-0.09470.3010.3113-0.11780.04220.3106-0.03680.04960.4462-0.05910.3324-9.725113.7821-35.2614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 31:41)
2X-RAY DIFFRACTION2chain A and (resseq 58:524 or resseq 1000:1001 or resseq 2000 or resseq 3000:3008 or resseq 4000:4008)
3X-RAY DIFFRACTION3chain A and (resseq 525:570 or resseq 5000)
4X-RAY DIFFRACTION4chain A and (resseq 571:662)
5X-RAY DIFFRACTION5chain B and (resseq 32:41)
6X-RAY DIFFRACTION6chain B and (resseq 56:524 or resseq 1000 or resseq 2000:2008 or resseq 3000:3002 or resseq 4000 or resseq 5000:5008)
7X-RAY DIFFRACTION7chain B and (resseq 525:570 or resseq 6000:6001)
8X-RAY DIFFRACTION8chain B and (resseq 571:663)

+
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