[English] 日本語
Yorodumi
- EMDB-75407: Dimeric complex of VEGF, VEGFR2 and Neuropilin 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-75407
TitleDimeric complex of VEGF, VEGFR2 and Neuropilin 1
Map data
Sample
  • Complex: dimeric complex of VEGF, VEGFR2 and Neuropilin 1
    • Protein or peptide: Isoform VEGF-1 of Vascular endothelial growth factor A, long form
    • Protein or peptide: Vascular endothelial growth factor receptor 2
    • Protein or peptide: Neuropilin-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
KeywordsVEGF / VEGFR / neuropilin / SIGNALING PROTEIN
Function / homology
Function and homology information


VEGF ligand-receptor interactions / VEGF binds to VEGFR leading to receptor dimerization / Neuropilin interactions with VEGF and VEGFR / cell migration involved in coronary vasculogenesis / trigeminal nerve morphogenesis / VEGFR2 mediated cell proliferation / Signal transduction by L1 / regulation of axon extension involved in axon guidance / regulation of endothelial cell differentiation / basal dendrite development ...VEGF ligand-receptor interactions / VEGF binds to VEGFR leading to receptor dimerization / Neuropilin interactions with VEGF and VEGFR / cell migration involved in coronary vasculogenesis / trigeminal nerve morphogenesis / VEGFR2 mediated cell proliferation / Signal transduction by L1 / regulation of axon extension involved in axon guidance / regulation of endothelial cell differentiation / basal dendrite development / otic placode development / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / basal dendrite arborization / regulation of endothelial cell proliferation / positive regulation of smooth muscle cell chemotaxis / dichotomous subdivision of terminal units involved in salivary gland branching / retina vasculature morphogenesis in camera-type eye / vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / VEGF-A complex / cellular stress response to acid chemical / positive regulation of nitric oxide-cGMP mediated signal transduction / trigeminal nerve structural organization / sensory neuron axon guidance / positive regulation of lymphangiogenesis / facial nerve structural organization / negative regulation of axon extension involved in axon guidance / vascular endothelial growth factor receptor 1 binding / negative regulation of adherens junction organization / branchiomotor neuron axon guidance / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / protein localization to early endosome / blood vessel endothelial cell differentiation / primitive erythrocyte differentiation / positive regulation of mast cell chemotaxis / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / post-embryonic camera-type eye development / regulation of bone development / lymph vessel morphogenesis / 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 / bone trabecula formation / axon extension involved in axon guidance / renal artery morphogenesis / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cellular response to hydrogen sulfide / coronary vein morphogenesis / positive regulation of signal transduction / cardiac vascular smooth muscle cell development / neurofilament / sympathetic neuron projection extension / lymphangiogenesis / endochondral bone growth / vascular endothelial growth factor binding / motor neuron migration / regulation of vascular endothelial growth factor receptor signaling pathway / angiogenesis involved in coronary vascular morphogenesis / postsynapse organization / vascular endothelial growth factor receptor-2 signaling pathway / endothelial tube morphogenesis / endocardium development / retina vasculature development in camera-type eye / endothelium development / neural crest cell migration involved in autonomic nervous system development / sympathetic ganglion development / axonogenesis involved in innervation / lung vasculature development / regulation of hematopoietic progenitor cell differentiation / vascular endothelial growth factor receptor activity / eye photoreceptor cell development / positive regulation of axon extension involved in axon guidance / post-embryonic camera-type eye morphogenesis / bone trabecula morphogenesis / endothelial cell chemotaxis / positive regulation of protein localization to early endosome / endothelial cell differentiation / positive regulation of trophoblast cell migration / positive regulation of long-term neuronal synaptic plasticity / Platelet degranulation / negative regulation of axon extension / lymph vessel development / positive regulation of vasculogenesis / vascular wound healing / positive regulation of epithelial tube formation / neuropilin signaling pathway / neuropilin binding / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / sympathetic nervous system development / camera-type eye morphogenesis / positive regulation of branching involved in ureteric bud morphogenesis
Similarity search - Function
Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / Vascular endothelial growth factor receptor 2 (VEGFR2) / VEGFR-2, transmembrane domain / : / : ...Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / Vascular endothelial growth factor receptor 2 (VEGFR2) / VEGFR-2, transmembrane domain / : / : / : / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / VEGFR1-3, N-terminal Ig-like domain / VEGFR-1-like, immunoglobulin-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 / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / : / Tyrosine-protein kinase, receptor class III, conserved site / MAM domain, meprin/A5/mu / Receptor tyrosine kinase class III signature. / MAM domain / MAM domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / Coagulation factor 5/8 C-terminal domain, discoidin domain / CUB domain / Spermadhesin, CUB domain superfamily / CUB domain profile. / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Cystine-knot cytokine / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Galactose-binding-like domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Concanavalin A-like lectin/glucanase domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Vascular endothelial growth factor receptor 2 / Neuropilin-1 / Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsChen L / Bai X / Zhang X
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130289 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM156386 United States
Robert A. Welch FoundationI-1702 United States
Robert A. Welch FoundationI-1944 United States
CitationJournal: To Be Published
Title: Mechanisms of VEGFR2 activation by VEGF, neuropilin and heparin
Authors: Chen L / Bai X / Zhang X
History
DepositionFeb 3, 2026-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_75407.png

Downloads & links

-
Map

FileDownload / File: emd_75407.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 330 pix.
= 356.4 Å		1.08 Å/pix.
x 330 pix.
= 356.4 Å		1.08 Å/pix.
x 330 pix.
= 356.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.040489085 - 0.08620506
Average (Standard dev.)0.000099932266 (±0.0016584942)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 356.40002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_75407_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_75407_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : dimeric complex of VEGF, VEGFR2 and Neuropilin 1

EntireName: dimeric complex of VEGF, VEGFR2 and Neuropilin 1
Components
  • Complex: dimeric complex of VEGF, VEGFR2 and Neuropilin 1
    • Protein or peptide: Isoform VEGF-1 of Vascular endothelial growth factor A, long form
    • Protein or peptide: Vascular endothelial growth factor receptor 2
    • Protein or peptide: Neuropilin-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

-
Supramolecule #1: dimeric complex of VEGF, VEGFR2 and Neuropilin 1

SupramoleculeName: dimeric complex of VEGF, VEGFR2 and Neuropilin 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 400 KDa

-
Macromolecule #1: Isoform VEGF-1 of Vascular endothelial growth factor A, long form

MacromoleculeName: Isoform VEGF-1 of Vascular endothelial growth factor A, long form
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 20.787742 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ELEHHHHHHH HAPTTEGEQK SHEVIKFMDV YQRSYCRPIE TLVDIFQEYP DEIEYIFKPS CVPLMRCAGC CNDEALECVP TSESNITMQ IMRIKPHQSQ HIGEMSFLQH SRCECRPKKD RTKPENHCEP CSERRKHLFV QDPQTCKCSC KNTDSRCKAR Q LELNERTC RCDKPRR

UniProtKB: Vascular endothelial growth factor A, long form

-
Macromolecule #2: Vascular endothelial growth factor receptor 2

MacromoleculeName: Vascular endothelial growth factor receptor 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 84.499039 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ELEASVGLPG DFLHPPKLST QKDILTILAN TTLQITCRGQ RDLDWLWPNA QRDSEERVLV TECGGGDSIF CKTLTIPRVV GNDTGAYKC SYRDVDIAST VYVYVRDYRS PFIASVSDQH GIVYITENKN KTVVIPCRGS ISNLNVSLCA RYPEKRFVPD G NRISWDSE ...String:
ELEASVGLPG DFLHPPKLST QKDILTILAN TTLQITCRGQ RDLDWLWPNA QRDSEERVLV TECGGGDSIF CKTLTIPRVV GNDTGAYKC SYRDVDIAST VYVYVRDYRS PFIASVSDQH GIVYITENKN KTVVIPCRGS ISNLNVSLCA RYPEKRFVPD G NRISWDSE IGFTLPSYMI SYAGMVFCEA KINDETYQSI MYIVVVVGYR IYDVILSPPH EIELSAGEKL VLNCTARTEL NV GLDFTWH SPPSKSHHKK IVNRDVKPFP GTVAKMFLST LTIESVTKSD QGEYTCVASS GRMIKRNRTF VRVHTKPFIA FGS GMKSLV EATVGSQVRI PVKYLSYPAP DIKWYRNGRP IESNYTMIVG DELTIMEVTE RDAGNYTVIL TNPISMEKQS HMVS LVVNV PPQIGEKALI SPMDSYQYGT MQTLTCTVYA NPPLHHIQWY WQLEEACSYR PGQTSPYACK EWRHVEDFQG GNKIE VTKN QYALIEGKNK TVSTLVIQAA NVSALYKCEA INKAGRGERV ISFHVIRGPE ITVQPAAQPT EQESVSLLCT ADRNTF ENL TWYKLGSQAT SVHMGESLTP VCKNLDALWK LNGTMFSNST NDILIVAFQN ASLQDQGDYV CSAQDKKTKK RHCLVKQ LI ILERMAPMIT GNLENQTTTI GETIEVTCPA SGNPTPHITW FKDNETLVED SGIVLRDGNR NLTIRRVRKE DGGLYTCQ A CNVLGCARAE TLFIIEGAQE KTNGTHHHHH HHH

UniProtKB: Vascular endothelial growth factor receptor 2

-
Macromolecule #3: Neuropilin-1

MacromoleculeName: Neuropilin-1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 95.312578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ELEFRSDKCG GTIKIENPGY LTSPGYPHSY HPSEKCEWLI QAPEPYQRIM INFNPHFDLE DRDCKYDYVE VIDGENEGGR LWGKFCGKI APSPVVSSGP FLFIKFVSDY ETHGAGFSIR YEIFKRGPEC SQNYTAPTGV IKSPGFPEKY PNSLECTYII F APKMSEII ...String:
ELEFRSDKCG GTIKIENPGY LTSPGYPHSY HPSEKCEWLI QAPEPYQRIM INFNPHFDLE DRDCKYDYVE VIDGENEGGR LWGKFCGKI APSPVVSSGP FLFIKFVSDY ETHGAGFSIR YEIFKRGPEC SQNYTAPTGV IKSPGFPEKY PNSLECTYII F APKMSEII LEFESFDLEQ DSNPPGGMFC RYDRLEIWDG FPEVGPHIGR YCGQKTPGRI RSSSGVLSMV FYTDSAIAKE GF SANYSVL QSSISEDFKC MEALGMESGE IHSDQITASS QYGTNWSVER SRLNYPENGW TPGEDSYKEW IQVDLGLLRF VTA VGTQGA ISKETKKKYY VKTYRVDISS NGEDWISLKE GNKAIIFQGN TNPTDVVLGV FSKPLITRFV RIKPVSWETG ISMR FEVYG CKITDYPCSG MLGMVSGLIS DSQITASNQA DRNWMPENIR LVTSRTGWAL PPSPHPYTNE WLQVDLGDEK IVRGV IIQG GKHRENKVFM RKFKIAYSNN GSDWKTIMDD SKRKAKSFEG NNNYDTPELR TFSPLSTRFI RIYPERATHS GLGLRM ELL GCEVEAPTAG PTTPNGNPVD ECDDDQANCH SGTGDDFQLT GGTTVLATEK PTIIDSTIQS EFPTYGFNCE FGWGSHK TF CHWEHDSHAQ LRWSVLTSKT GPIQDHTGDG NFIYSQADEN QKGKVARLVS PVVYSQSSAH CMTFWYHMSG SHVGTLRV K LRYQKPEEYD QLVWMVVGHQ GDHWKEGRVL LHKSLKLYQV IFEGEIGKGN LGGIAVDDIS INNHISQEDC AKPTDLDKK NTEIKIDETG STPGYEGEGE GDKNISRKPG NVLKTLDGTH HHHHHHH

UniProtKB: Neuropilin-1

-
Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: NITROGEN

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 64468
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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