[English] 日本語
Yorodumi
- PDB-6fkn: Drosophila Plexin A in complex with Semaphorin 1b -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fkn
TitleDrosophila Plexin A in complex with Semaphorin 1b
Components
  • MIP07328p
  • Plexin A, isoform A
KeywordsSIGNALING PROTEIN / semaphorin / plexin / sema domain / cis interaction
Function / homology
Function and homology information


RHOD GTPase cycle / semaphorin-plexin signaling pathway involved in regulation of photoreceptor cell axon guidance / Sema3A PAK dependent Axon repulsion / CRMPs in Sema3A signaling / G alpha (12/13) signalling events / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Other semaphorin interactions / guanylate cyclase activator activity / Sema4D induced cell migration and growth-cone collapse / embryonic development via the syncytial blastoderm ...RHOD GTPase cycle / semaphorin-plexin signaling pathway involved in regulation of photoreceptor cell axon guidance / Sema3A PAK dependent Axon repulsion / CRMPs in Sema3A signaling / G alpha (12/13) signalling events / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Other semaphorin interactions / guanylate cyclase activator activity / Sema4D induced cell migration and growth-cone collapse / embryonic development via the syncytial blastoderm / semaphorin receptor binding / sensory neuron axon guidance / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of axon extension involved in axon guidance / semaphorin receptor complex / positive regulation of guanylate cyclase activity / chemorepellent activity / semaphorin receptor activity / negative regulation of cell adhesion / axon midline choice point recognition / negative chemotaxis / positive regulation of axonogenesis / regulation of GTPase activity / semaphorin-plexin signaling pathway / regulation of cell migration / GTPase activator activity / 14-3-3 protein binding / axon guidance / heparin binding / regulation of cell shape / Ras protein signal transduction / positive regulation of cell migration / membrane / plasma membrane / cytosol
Similarity search - Function
Semaphorin-1A, sema domain / Semaphorin / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain ...Semaphorin-1A, sema domain / Semaphorin / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / Rho GTPase activation protein / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
MIP07328p / Plexin A, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.801 Å
AuthorsRozbesky, D. / Harlos, K. / Jones, E.Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKB5R00120 United Kingdom
CitationJournal: Embo J. / Year: 2020
Title: Structural basis of semaphorin-plexin cis interaction.
Authors: Rozbesky, D. / Verhagen, M.G. / Karia, D. / Nagy, G.N. / Alvarez, L. / Robinson, R.A. / Harlos, K. / Padilla-Parra, S. / Pasterkamp, R.J. / Jones, E.Y.
History
DepositionJan 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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 / 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_validate_chiral / 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.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 / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _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 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 17, 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
A: Plexin A, isoform A
B: MIP07328p
C: Plexin A, isoform A
D: MIP07328p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,30814
Polymers285,8244
Non-polymers4,48410
Water0
1
A: Plexin A, isoform A
B: MIP07328p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,9117
Polymers142,9122
Non-polymers1,9995
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Plexin A, isoform A
D: MIP07328p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,3977
Polymers142,9122
Non-polymers2,4855
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.630, 153.630, 425.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain B and (resid 53 through 292 or resid 295...
211(chain D and (resid 53 through 292 or resid 295...
112chain A
212(chain C and (resid 62 through 126 or resid 128 through 1003))

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.978135125924, 0.044070146626, 0.203247380329), (-0.0197492321061, 0.953190655836, -0.301724280524), (-0.207030537036, -0.299141096814, -0.931478910621)-11.9052323741, 9.85824068066, 9.69741043937
2given(-0.985522480265, 0.0382711563491, 0.165168881704), (-0.0126434639888, 0.954888016128, -0.296696847765), (-0.169072717225, -0.294489720105, -0.940579726043)-10.5783105889, 9.69696305674, 10.018559383

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Plexin A, isoform A


Mass: 78699.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: PlexA, BcDNA:GM05237, D-Plex A, Dmel\CG11081, DPlexA, lincRNA.927, plex, plex A, Plex1, plexA, PlexA1, CG11081, Dmel_CG11081
Variant: isoform A / Plasmid: pHLSec / Cell (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9V491
#2: Protein MIP07328p / Sema-1b / isoform A / isoform B / isoform C / Semaphorin-like


Mass: 64212.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Sema1b, Sema-1b, Sema-1b-RB, semaphorin-like, CG6446, Dmel_CG6446
Plasmid: pHLSec / Cell (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q7KK54

-
Sugars , 4 types, 10 molecules

#3: 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-e1WURCSPDB2Glycan 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]{}}}}}LINUCSPDB-CARE
#6: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES and 12% (w/v) PEG 20 000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.0719 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0719 Å / Relative weight: 1
ReflectionResolution: 4.801→133.047 Å / Num. obs: 15309 / % possible obs: 99.9 % / Redundancy: 20.9 % / Biso Wilson estimate: 217.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.339 / Net I/σ(I): 7.41
Reflection shellResolution: 4.801→4.97 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.13rc2_2986: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KFM

6kfm


Resolution: 4.801→133.047 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.297 819 5.35 %
Rwork0.2848 --
obs0.2854 15307 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.801→133.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15305 0 295 0 15600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515984
X-RAY DIFFRACTIONf_angle_d0.81121770
X-RAY DIFFRACTIONf_dihedral_angle_d12.0565915
X-RAY DIFFRACTIONf_chiral_restr0.0632540
X-RAY DIFFRACTIONf_plane_restr0.0052760
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B3736X-RAY DIFFRACTIONPOSITIONAL
12D3736X-RAY DIFFRACTIONPOSITIONAL0.946
21A3965X-RAY DIFFRACTIONPOSITIONAL
22C3965X-RAY DIFFRACTIONPOSITIONAL0.002
Refinement TLS params.Method: refined / Origin x: -2.4413 Å / Origin y: 43.7016 Å / Origin z: 1.2018 Å
111213212223313233
T2.2291 Å2-0.0028 Å2-0.1705 Å2-2.3678 Å20.1186 Å2--2.32 Å2
L0.5064 °2-0.046 °2-0.4969 °2-0.7743 °20.198 °2--1.1783 °2
S-0.0218 Å °0.0953 Å °-0.0219 Å °0.2378 Å °-0.0047 Å °0.2411 Å °0.0811 Å °-0.3514 Å °0.073 Å °
Refinement TLS groupSelection details: all

+
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