[English] 日本語
Yorodumi
- PDB-6zcd: VEGF-A 13:107 crystallized with 1C bicyclic peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zcd
TitleVEGF-A 13:107 crystallized with 1C bicyclic peptide
Components
  • Derived from V114 peptide
  • Vascular endothelial growth factor A
KeywordsPEPTIDE BINDING PROTEIN / growth factor / peptide ligand / lactam bridge / alpha-helix stabilization / SIGNALING PROTEIN
Function / homology
Function and homology information


basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier ...basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / post-embryonic camera-type eye development / primitive erythrocyte differentiation / positive regulation of protein kinase C signaling / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / negative regulation of blood-brain barrier permeability / VEGF-activated neuropilin signaling pathway / bone trabecula formation / positive regulation of vascular endothelial growth factor signaling pathway / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / lung vasculature development / lymphangiogenesis / eye photoreceptor cell development / endothelial cell chemotaxis / motor neuron migration / positive regulation of trophoblast cell migration / positive regulation of epithelial tube formation / vascular endothelial growth factor receptor-2 signaling pathway / VEGF binds to VEGFR leading to receptor dimerization / regulation of nitric oxide mediated signal transduction / positive regulation of axon extension involved in axon guidance / vascular wound healing / positive regulation of protein localization to early endosome / regulation of hematopoietic progenitor cell differentiation / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of branching involved in ureteric bud morphogenesis / camera-type eye morphogenesis / neuropilin binding / induction of positive chemotaxis / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / vascular endothelial growth factor receptor 2 binding / tube formation / positive regulation of vascular permeability / dopaminergic neuron differentiation / commissural neuron axon guidance / negative regulation of epithelial to mesenchymal transition / platelet-derived growth factor receptor binding / surfactant homeostasis / extracellular matrix binding / cell migration involved in sprouting angiogenesis / cardiac muscle cell development / epithelial cell maturation / sprouting angiogenesis / positive regulation of positive chemotaxis / endothelial cell proliferation / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of leukocyte migration / vascular endothelial growth factor signaling pathway / positive regulation of p38MAPK cascade / positive regulation of endothelial cell chemotaxis / artery morphogenesis / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of DNA biosynthetic process / retinal ganglion cell axon guidance / positive regulation of neuroblast proliferation / positive chemotaxis / negative regulation of fat cell differentiation / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of sprouting angiogenesis / chemoattractant activity / outflow tract morphogenesis / positive regulation of focal adhesion assembly / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / macrophage differentiation / fibronectin binding / positive regulation of cell division / positive regulation of cell adhesion / neuroblast proliferation / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / mammary gland alveolus development / vasculogenesis / positive regulation of osteoblast differentiation / vascular endothelial growth factor receptor signaling pathway / heart morphogenesis / ovarian follicle development / cell maturation / homeostasis of number of cells within a tissue / positive regulation of protein autophosphorylation / positive regulation of endothelial cell proliferation / epithelial cell differentiation / lactation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors
Similarity search - Function
Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding 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 / Cystine-knot cytokine
Similarity search - Domain/homology
PHOSPHATE ION / Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGaucher, J.-F. / Broussy, S. / Reille-Seroussi, M.
CitationJournal: Chemistry / Year: 2022
Title: Structural and ITC Characterization of Peptide-Protein Binding: Thermodynamic Consequences of Cyclization Constraints, a Case Study on Vascular Endothelial Growth Factor Ligands.
Authors: Gaucher, J.F. / Reille-Seroussi, M. / Broussy, S.
History
DepositionJun 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
P: Derived from V114 peptide
V: Vascular endothelial growth factor A
W: Vascular endothelial growth factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8829
Polymers24,1963
Non-polymers6866
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, Kd VEGF:peptide 1C = 38nM in hepes/NaOH 50mM pH 7.5 NaCl 150mM
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-74 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.644, 55.699, 77.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein/peptide Derived from V114 peptide


Mass: 1938.228 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DERIVED FROM V114 PEPTIDE FROM GENENTECH INC.; CG of ASP 14 and NZ of LYS 10 covalently linked by lactam bridge;
Source: (synth.) synthetic construct (others)
#2: Protein Vascular endothelial growth factor A / VEGF-A / Vascular permeability factor / VPF


Mass: 11128.835 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VEGFA, VEGF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: P15692
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: (VEGF)2:2 PEPTIDE_1C COMPLEX PURIFIED ON SEC AND CONCENTRATED AT 13.5MG/ML IN TRIS/HCL 10MM PH 8.5. MIX 1UL OF COMPLEX WITH 1 UL OF RESERVOIR : NAOAC/HCL 100MM PH 4.5 / MPD 35% (V/V) / (NH4)2PO4 150MM

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.272 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.272 Å / Relative weight: 1
ReflectionResolution: 1.8→53.64 Å / Num. obs: 22094 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 23.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.047 / Rrim(I) all: 0.107 / Χ2: 0.94 / Net I/σ(I): 11.5
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 10 % / Rmerge(I) obs: 0.902 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1271 / CC1/2: 0.957 / Rpim(I) all: 0.419 / Rrim(I) all: 0.951 / Χ2: 0.76 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
MxCuBEdata collection
XDSdata reduction
SCALAdata scaling
PHENIX1.18_3855phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FLT

1flt


Resolution: 1.8→45.17 Å / SU ML: 0.2205 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4028
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2418 1127 5.14 %
Rwork0.1899 20819 -
obs0.1924 21946 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.36 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1669 0 45 124 1838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011781
X-RAY DIFFRACTIONf_angle_d1.14172408
X-RAY DIFFRACTIONf_chiral_restr0.0629247
X-RAY DIFFRACTIONf_plane_restr0.0071313
X-RAY DIFFRACTIONf_dihedral_angle_d20.0496687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.880.34751360.29342533X-RAY DIFFRACTION99.44
1.88-1.980.29671420.25072565X-RAY DIFFRACTION99.23
1.98-2.110.25811400.20962545X-RAY DIFFRACTION99.59
2.11-2.270.26071400.19492586X-RAY DIFFRACTION99.74
2.27-2.50.21791390.18972580X-RAY DIFFRACTION99.31
2.5-2.860.27651530.19852598X-RAY DIFFRACTION99.85
2.86-3.60.2591520.18062608X-RAY DIFFRACTION99.14
3.6-45.170.19031250.1682804X-RAY DIFFRACTION99.93
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)
15.303324042360.63523265238-5.158564990795.90039908263-1.068240391245.04849332713-0.1492436938460.287799532559-0.00557581299887-0.253174694182-0.1799505001290.657313253388-0.20107467819-0.8089246003680.3023952491010.3811800783490.00410739738414-0.03802667363770.27711814397-0.02991824514720.30097847925821.16799441956.951366186038.05202862445
24.863609678425.00831476032-4.910978153645.1552907764-5.03664085755.015044487770.303362152678-0.383574296321-0.4104411615210.86101399529-0.494426759307-0.684364676174-0.2348625419380.1713151741560.2846513065710.446569769601-0.0221854190137-0.0239956665120.2202491217310.02553761070220.26954392988330.998259523322.0063808867-6.99147110945
31.014435725871.3620060094-0.9910542169869.19088607882-3.579931809113.65699063127-0.0224663916239-0.0537695558858-0.162029527177-0.0988984506458-0.38856888814-0.9256290518650.3672900599790.4539704410260.4354953663320.3451921915070.0480784224586-0.02072554456580.3163955540080.02952633017670.2654401154733.418082714320.1517920309-7.85758231221
40.8872354240670.632479576335-0.6152624095118.09291369005-3.115001959323.573881342160.09307692482050.03206719779380.00140025931665-0.381562465025-0.248756105241-0.2396877369770.005656475505040.235345590.1677482570730.3452283012480.02695639346070.009161282964310.235387384010.02812651440150.16918778230430.509329625326.8281062217-15.0391764036
53.66943449214-2.57997262801-3.062275956094.127409730970.01584175533374.53518462970.1515227382460.178194208617-0.419531545057-0.315031210519-0.299897760182-0.01412356385062.165718797220.57475372903-0.1062984284780.8337371174490.1014763479610.008595620480530.354824521107-0.01513284138920.31116851643829.02000288914.63791484497-9.59928517604
68.412493807281.732479313375.743338226246.372216714321.883674221754.53524716927-0.149938450136-0.2696413065640.1325035557950.328253773594-0.1162550191330.507730345086-0.406540634393-1.043845189120.3319214820650.3845962037370.02846755314760.0655958384170.256790640856-0.04808998586110.26988900134722.812801429833.0526514186-7.79638975616
77.50553888161-5.78575109835.308166766279.68580610891-6.249625562958.762962069020.1763437379930.4736378018130.00370348671844-0.270929347245-0.17675933046-0.0734230312896-0.07481612410280.8723179870410.05624140534110.416198307914-0.04209474934850.06427905717530.319805781023-0.04646322011010.19383417445331.019836535616.18238390116.24324739462
88.705464921061.39864875143-5.46438798951.57356124436-3.445322585938.3144764371-0.7948949867850.283963839133-0.773497895915-0.725165804801-0.4371047154470.6485735230460.878868896626-0.7019437234350.527188672860.7179579290790.102729080441-0.09904468206980.881843203631-0.4644041621080.73114558147340.33957371996.1764937159714.1756710733
91.0299632774-0.8880246319390.3824238925713.11160506059-3.519110685084.629129304220.07541420893460.05968954090430.177222547765-0.0865726518383-0.170159126405-0.270200788322-0.3797160620070.3829506165930.1222076838320.399757798149-0.01433192181630.02968416291560.296006288050.003670058058180.18743164846431.280540905119.70042639175.13788816749
102.314025242711.67311956647-0.6563943189274.242418698570.02731371188482.77829901730.0511051498441-0.0556501215317-0.2399733836610.3551138727840.00426934369001-0.2338166054570.2014809262470.506121020845-0.05415665440720.4150846204650.053248059624-0.04377274786430.327010730693-0.006891077908430.18855300163730.864501561911.935563404313.8042922482
111.164828546560.94992097895-0.3462676717814.22854966707-3.986289005264.60330216030.0760711783911-0.09075043097470.08534838681860.305438842668-0.008189134945780.176963369346-0.3704662365770.343515058429-0.01096958801240.390840212044-0.01644949517910.01668069728070.294820543308-0.03063075131350.18741247713229.643030904519.74313892613.1572726326
128.11214560038-4.711603303613.998568237147.24605000633-3.347840920579.30271839809-0.1630538556320.4154572004971.73200070073-0.576419757433-0.576417381919-0.714713050809-2.96078504132-0.1914679564080.78482275541.44064428885-0.007660361245870.08422154245840.587215091954-0.05062595130740.65622646943727.436484301843.00181015781.00138870767
133.754177867371.28852738283-2.245983998490.442132258402-0.7709479293951.34347828483-0.2671956812350.7010144927562.180482564870.3035533406980.0791135228290.502578094856-3.154230240790.002775688048620.2663173050591.718689266580.0496811151182-0.3706477885550.6272892647160.08851089830540.82277151401224.479933613146.3040843586-8.21855185435
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'V' and (resid 13 through 26 )VB13 - 261 - 14
22chain 'V' and (resid 27 through 38 )VB27 - 3815 - 26
33chain 'V' and (resid 39 through 65 )VB39 - 6527 - 56
44chain 'V' and (resid 66 through 99 )VB66 - 9957 - 90
55chain 'V' and (resid 100 through 107 )VB100 - 10791 - 98
66chain 'W' and (resid 13 through 26 )WC13 - 261 - 14
77chain 'W' and (resid 27 through 38 )WC27 - 3815 - 26
88chain 'W' and (resid 39 through 45 )WC39 - 4527 - 33
99chain 'W' and (resid 46 through 65 )WC46 - 6534 - 53
1010chain 'W' and (resid 66 through 88 )WC66 - 8854 - 78
1111chain 'W' and (resid 89 through 107 )WC89 - 10779 - 97
1212chain 'P' and (resid 1 through 8 )PA1 - 81 - 8
1313chain 'P' and (resid 9 through 15 )PA9 - 159 - 15

+
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://pdbjlvh1.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