[English] 日本語
Yorodumi
- PDB-4gza: Complex of mouse Plexin A2 - Semaphorin 3A - Neuropilin-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gza
TitleComplex of mouse Plexin A2 - Semaphorin 3A - Neuropilin-1
Components
  • Neuropilin-1
  • Plexin-A2
  • Semaphorin-3A
KeywordsSIGNALING PROTEIN / ternary complex / multi-domain / mammalian / cell-cell signaling / glycosilation / transmembrane
Function / homology
Function and homology information


Neurophilin interactions with VEGF and VEGFR / neural crest cell migration involved in sympathetic nervous system development / cell migration involved in coronary vasculogenesis / trigeminal nerve morphogenesis / Signal transduction by L1 / cerebellar granule cell precursor tangential migration / regulation of axon extension involved in axon guidance / CRMPs in Sema3A signaling / basal dendrite development / otic placode development ...Neurophilin interactions with VEGF and VEGFR / neural crest cell migration involved in sympathetic nervous system development / cell migration involved in coronary vasculogenesis / trigeminal nerve morphogenesis / Signal transduction by L1 / cerebellar granule cell precursor tangential migration / regulation of axon extension involved in axon guidance / CRMPs in Sema3A signaling / basal dendrite development / otic placode development / positive regulation of smooth muscle cell chemotaxis / protein localization to early endosome / Sema3A PAK dependent Axon repulsion / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / retina vasculature morphogenesis in camera-type eye / regulation of vascular endothelial growth factor receptor signaling pathway / vestibulocochlear nerve structural organization / semaphorin receptor binding / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / epithelial cell migration / neurofilament / postsynapse organization / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / branchiomotor neuron axon guidance / renal artery morphogenesis / positive regulation of male gonad development / cerebellar climbing fiber to Purkinje cell synapse / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / maintenance of synapse structure / axon extension involved in axon guidance / VEGF-activated neuropilin signaling pathway / synaptic target recognition / negative regulation of axon extension involved in axon guidance / sympathetic neuron projection extension / blood vessel endothelial cell migration / negative regulation of epithelial cell migration / vascular endothelial growth factor binding / retina vasculature development in camera-type eye / endothelial cell chemotaxis / motor neuron migration / limb bud formation / axonogenesis involved in innervation / sympathetic ganglion development / neural crest cell migration involved in autonomic nervous system development / positive regulation of axon extension involved in axon guidance / positive regulation of platelet-derived growth factor receptor signaling pathway / vascular endothelial growth factor receptor activity / negative regulation of axon extension / nerve development / semaphorin receptor complex / positive regulation of neuron migration / olfactory bulb development / angiogenesis involved in coronary vascular morphogenesis / pharyngeal system development / neuropilin signaling pathway / sympathetic nervous system development / neuropilin binding / coronary artery morphogenesis / hepatocyte growth factor receptor signaling pathway / substrate-dependent cell migration, cell extension / outflow tract septum morphogenesis / chemorepellent activity / semaphorin receptor activity / commissural neuron axon guidance / negative regulation of cell adhesion / axon extension / positive regulation of vascular associated smooth muscle cell migration / motor neuron axon guidance / cell migration involved in sprouting angiogenesis / axonal fasciculation / regulation of Cdc42 protein signal transduction / sprouting angiogenesis / dendrite morphogenesis / neural tube development / neural crest cell migration / positive regulation of filopodium assembly / artery morphogenesis / centrosome localization / negative chemotaxis / positive regulation of cell migration involved in sprouting angiogenesis / branching involved in blood vessel morphogenesis / positive regulation of axonogenesis / cellular response to hepatocyte growth factor stimulus / retinal ganglion cell axon guidance / positive chemotaxis / dendrite development / growth factor binding / sorting endosome / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / platelet-derived growth factor receptor signaling pathway / endothelial cell migration
Similarity search - Function
Semaphorin-3A, sema domain / Plexin-A2, sema domain / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Semaphorin / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain ...Semaphorin-3A, sema domain / Plexin-A2, sema domain / IL-1Ra-like, immunoglobulin domain / Immunoglobulin 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 / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / : / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Plexin family / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Plexin repeat / Plexin repeat / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / Sema domain / CUB domain profile. / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / Spermadhesin, CUB domain superfamily / Coagulation factor 5/8 C-terminal domain, discoidin domain / IPT/TIG domain / Coagulation factors 5/8 type C domain (FA58C) profile. / ig-like, plexins, transcription factors / F5/8 type C domain / Rho GTPase activation protein / Coagulation factor 5/8 C-terminal domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / Galactose-binding-like domain superfamily / Immunoglobulin E-set / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Semaphorin-3A / Plexin-A2 / Neuropilin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7 Å
AuthorsJanssen, B.J.C. / Malinauskas, T. / Siebold, C. / Jones, E.Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Neuropilins lock secreted semaphorins onto plexins in a ternary signaling complex.
Authors: Janssen, B.J.C. / Malinauskas, T. / Weir, G.A. / Cader, M.Z. / Siebold, C. / Jones, E.Y.
History
DepositionSep 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Plexin-A2
B: Plexin-A2
C: Plexin-A2
D: Plexin-A2
E: Plexin-A2
F: Plexin-A2
G: Semaphorin-3A
H: Neuropilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)582,3649
Polymers582,3248
Non-polymers401
Water00
1
A: Plexin-A2
B: Plexin-A2
C: Plexin-A2
D: Plexin-A2
E: Plexin-A2
F: Plexin-A2
G: Semaphorin-3A
H: Neuropilin-1
hetero molecules

A: Plexin-A2
B: Plexin-A2
C: Plexin-A2
D: Plexin-A2
E: Plexin-A2
F: Plexin-A2
G: Semaphorin-3A
H: Neuropilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,164,72818
Polymers1,164,64816
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Unit cell
Length a, b, c (Å)191.632, 293.604, 252.176
Angle α, β, γ (deg.)90.00, 106.38, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Plexin-A2 / Plex 2 / Plexin-2


Mass: 75934.914 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 33-703
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plxna2, Kiaa0463 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P70207
#2: Protein Semaphorin-3A / Semaphorin III / Sema III / Semaphorin-D / Sema D


Mass: 61246.945 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-555
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sema3a, Semad, SemD / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O08665
#3: Protein Neuropilin-1 / A5 protein


Mass: 65467.652 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 22-586
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nrp1, Nrp / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P97333
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Sequence detailsTHE SEQUENCE OF CHAIN G IS BASED ON NCBI REFERENCE SEQUENCE: NP_033178.2. RESIDUE 475 IS A VAL IN ...THE SEQUENCE OF CHAIN G IS BASED ON NCBI REFERENCE SEQUENCE: NP_033178.2. RESIDUE 475 IS A VAL IN THIS DATABASE SEQUENCE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
15.8478.95
2
3
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop7.570mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2932vapor diffusion, sitting drop7.570mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, 1% v/v ethyl acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2933vapor diffusion, sitting drop7.570mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, 8% v/v acetonitrile , VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
31003
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I04-110.9173
SYNCHROTRONDiamond I0321.0719
SYNCHROTRONDiamond I0230.9795
Detector
TypeIDDetectorDate
DECTRIS PILATUS 2M1PIXELApr 15, 2011
DECTRIS PILATUS 6M2PIXELApr 20, 2011
ADSC QUANTUM 315r3CCDMay 5, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single bounce monochromatorSINGLE WAVELENGTHMx-ray1
2Double crystal monochromatorSINGLE WAVELENGTHMx-ray1
3Double crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91731
21.07191
30.97951
ReflectionResolution: 7→126 Å / Num. all: 20190 / Num. obs: 20176 / % possible obs: 95.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OKT, 1Q47, 4GZ9

3okt

1q47

4gz9


Resolution: 7→125.506 Å / SU ML: 1.03 / Cross valid method: THROUGHOUT / σ(F): -3 / Phase error: 29.14 / Stereochemistry target values: MLHL
Details: AUTHORS STATE THAT DUE TO THE LOW RESOLUTION OF THE DIFFRACTION DATA THE STRUCTURE WAS ONLY SUBJECTED TO RIGID BODY REFINEMENT WITH EACH DOMAIN AS RIGID BODY USING (PARTS OF) THE COORDINATES ...Details: AUTHORS STATE THAT DUE TO THE LOW RESOLUTION OF THE DIFFRACTION DATA THE STRUCTURE WAS ONLY SUBJECTED TO RIGID BODY REFINEMENT WITH EACH DOMAIN AS RIGID BODY USING (PARTS OF) THE COORDINATES OF PDB ENTRIES 3OKT, 1Q47 AND 4GZ9. AUTHORS HAVE NOT FURTHER REFINED THE RESULTING COORDINATES NOR CORRECTED RESULTING CLASHES BETWEEN ATOMS AND DEVIATING PEPTIDE LINKAGES BETWEEN DOMAINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2848 1009 5.05 %RANDOM
Rwork0.2847 ---
obs0.2847 20176 95.6 %-
all-20176 --
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 283.537 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-84.1244 Å2-0 Å2119.0039 Å2
2--17.4558 Å2-0 Å2
3---22.6768 Å2
Refinement stepCycle: LAST / Resolution: 7→125.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35654 0 1 0 35655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01436622
X-RAY DIFFRACTIONf_angle_d1.20249584
X-RAY DIFFRACTIONf_dihedral_angle_d13.07413337
X-RAY DIFFRACTIONf_chiral_restr0.0635452
X-RAY DIFFRACTIONf_plane_restr0.0086434
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
7.0004-7.17550.36191190.3727260894
7.1755-7.36950.36681680.3578266094
7.3695-7.58630.31881490.3447263194
7.5863-7.83110.30611580.3451258393
7.8311-8.1110.31851340.3312256590
8.111-8.43570.32091210.3213228781
8.4357-8.81950.31881330.2921239485
8.8195-9.28430.28781390.2803270095
9.2843-9.86580.26911320.2596265795
9.8658-10.62720.22871500.2527266795
10.6272-11.69590.25181270.2403273195
11.6959-13.38670.27641210.253264393
13.3867-16.85940.281300.2752245588
16.8594-125.52630.27391410.2832257591

+
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://pdbjlc1.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