[English] 日本語
Yorodumi
- PDB-5c7g: Crystal Structure of the b1 Domain of Human Neuropilin-1 in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c7g
TitleCrystal Structure of the b1 Domain of Human Neuropilin-1 in complex with a bicine molecule
ComponentsNeuropilin-1Neuropilin 1
KeywordsPROTEIN BINDING / Neuropilin-1 / Human / Blood Coagulation Factors / Cell Adhesion / Binding sites
Function / homology
Function and homology information


positive regulation of cytokine activity / endothelial tip cell fate specification / basal dendrite development / protein localization to early endosome / otic placode development / neurofilament / 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 ...positive regulation of cytokine activity / endothelial tip cell fate specification / basal dendrite development / protein localization to early endosome / otic placode development / neurofilament / 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 / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / postsynapse organization / branchiomotor neuron axon guidance / renal artery morphogenesis / axon extension involved in axon guidance / VEGF-activated neuropilin signaling pathway / negative regulation of axon extension involved in axon guidance / sympathetic neuron projection extension / motor neuron migration / Neurophilin interactions with VEGF and VEGFR / endothelial cell chemotaxis / vascular endothelial growth factor binding / sympathetic ganglion development / axonogenesis involved in innervation / neural crest cell migration involved in autonomic nervous system development / positive regulation of axon extension involved in axon guidance / CHL1 interactions / vascular endothelial growth factor receptor activity / substrate-dependent cell migration, cell extension / semaphorin receptor complex / regulation of vesicle-mediated transport / Signaling by ROBO receptors / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / angiogenesis involved in coronary vascular morphogenesis / hepatocyte growth factor receptor signaling pathway / neuropilin signaling pathway / coronary artery morphogenesis / outflow tract septum morphogenesis / regulation of Cdc42 protein signal transduction / semaphorin receptor activity / commissural neuron axon guidance / CRMPs in Sema3A signaling / motor neuron axon guidance / cell migration involved in sprouting angiogenesis / retinal ganglion cell axon guidance / artery morphogenesis / axonal fasciculation / sprouting angiogenesis / neural crest cell migration / positive regulation of filopodium assembly / branching involved in blood vessel morphogenesis / cellular response to hepatocyte growth factor stimulus / positive regulation of cell migration involved in sprouting angiogenesis / positive chemotaxis / cytokine binding / positive regulation of smooth muscle cell migration / growth factor binding / sorting endosome / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / platelet-derived growth factor receptor signaling pathway / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / vascular endothelial growth factor receptor signaling pathway / coreceptor activity / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / positive regulation of endothelial cell proliferation / GTPase activator activity / positive regulation of endothelial cell migration / Signal transduction by L1 / integrin-mediated signaling pathway / axon guidance / mitochondrial membrane / negative regulation of extrinsic apoptotic signaling pathway / animal organ morphogenesis / neuron migration / response to wounding / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell signaling / heparin binding / cytoplasmic vesicle / postsynaptic membrane / angiogenesis / negative regulation of neuron apoptotic process / Attachment and Entry / positive regulation of ERK1 and ERK2 cascade / receptor complex / early endosome
Similarity search - Function
Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / MAM domain profile. / CUB domain ...Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / MAM domain profile. / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Spermadhesin, CUB domain superfamily / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsDidierjean, C. / Jelsch, C.
CitationJournal: To Be Published
Title: Design, synthesis and biological evaluation of new peptidomimetic compounds targeting NRP-1 receptor TO BE PUBLISHED
Authors: Richard, M. / Pelligrini Moise, N. / Jelsch, C. / Maigret, B. / Didierjean, C. / Manival, X. / Charron, C.
History
DepositionJun 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neuropilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6063
Polymers18,4201
Non-polymers1862
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint-9 kcal/mol
Surface area7650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.280, 62.280, 85.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-530-

HOH

-
Components

#1: Protein Neuropilin-1 / Neuropilin 1 / Vascular endothelial cell growth factor 165 receptor


Mass: 18419.779 Da / Num. of mol.: 1 / Fragment: B1 DOMAIN, UNP residues 273-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP1, NRP, VEGF165R / Production host: Escherichia coli (E. coli) / References: UniProt: O14786
#2: Chemical ChemComp-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG550 mme 5%, PEG 20 000, 60mM MgCl2, Na-Bicine 100 mM, pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97967 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2013
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97967 Å / Relative weight: 1
ReflectionResolution: 1.45→39.2 Å / Num. obs: 30515 / % possible obs: 99.5 % / Redundancy: 12 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 24.9
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 10 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 3.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KEX

1kex


Resolution: 1.45→29.278 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1725 1999 6.55 %
Rwork0.1414 --
obs0.1435 30507 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→29.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1226 0 12 286 1524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081270
X-RAY DIFFRACTIONf_angle_d1.2671720
X-RAY DIFFRACTIONf_dihedral_angle_d17.662471
X-RAY DIFFRACTIONf_chiral_restr0.077187
X-RAY DIFFRACTIONf_plane_restr0.007218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48630.19351400.18771996X-RAY DIFFRACTION100
1.4863-1.52640.23081400.19281995X-RAY DIFFRACTION100
1.5264-1.57140.21591400.18711998X-RAY DIFFRACTION100
1.5714-1.62210.21021410.17532010X-RAY DIFFRACTION100
1.6221-1.680.19621430.16012028X-RAY DIFFRACTION100
1.68-1.74730.19031400.16631995X-RAY DIFFRACTION100
1.7473-1.82680.1751420.15012024X-RAY DIFFRACTION99
1.8268-1.92310.17421410.15892019X-RAY DIFFRACTION99
1.9231-2.04360.18511410.14952003X-RAY DIFFRACTION99
2.0436-2.20130.16451410.14042017X-RAY DIFFRACTION99
2.2013-2.42270.16571420.13522022X-RAY DIFFRACTION99
2.4227-2.77310.15981450.13972067X-RAY DIFFRACTION100
2.7731-3.49290.18671480.13412106X-RAY DIFFRACTION100
3.4929-29.2840.15351550.12672228X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 12.1908 Å / Origin y: 15.474 Å / Origin z: 20.3132 Å
111213212223313233
T0.1026 Å20.0019 Å2-0.0179 Å2-0.1125 Å20.0004 Å2--0.1138 Å2
L1.0458 °20.0941 °20.1454 °2-2.5691 °20.7228 °2--1.2908 °2
S0.0179 Å °-0.1036 Å °0.0285 Å °0.175 Å °-0.0239 Å °0.0064 Å °0.0551 Å °0.0258 Å °0.0105 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