[English] 日本語
Yorodumi
- PDB-3s1k: The Development of Peptide-based Tools for the Analysis of Angiog... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3s1k
TitleThe Development of Peptide-based Tools for the Analysis of Angiogenesis
Components
  • Vascular endothelial growth factor A
  • Z-domain
KeywordsSIGNALING PROTEIN / VEGF / cystine knot / Z-domain / phage-display / cystine-knot
Function / homology
Function and homology information


basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / VEGF-A complex / Signaling by VEGF / cellular stress response to acid chemical / positive regulation of lymphangiogenesis / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions ...basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / VEGF-A complex / Signaling by VEGF / cellular stress response to acid chemical / positive regulation of lymphangiogenesis / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / negative regulation of adherens junction organization / post-embryonic camera-type eye development / positive regulation of mast cell chemotaxis / lymph vessel morphogenesis / primitive erythrocyte differentiation / negative regulation of blood-brain barrier permeability / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / regulation of nitric oxide mediated signal transduction / VEGF-activated neuropilin signaling pathway / bone trabecula formation / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / lymphangiogenesis / lung vasculature development / vascular endothelial growth factor receptor-2 signaling pathway / positive regulation of epithelial tube formation / VEGF binds to VEGFR leading to receptor dimerization / motor neuron migration / positive regulation of trophoblast cell migration / positive regulation of axon extension involved in axon guidance / endothelial cell chemotaxis / eye photoreceptor cell development / vascular wound healing / positive regulation of protein localization to early endosome / regulation of hematopoietic progenitor cell differentiation / camera-type eye morphogenesis / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / neuropilin binding / positive regulation of branching involved in ureteric bud morphogenesis / induction of positive chemotaxis / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / transmembrane receptor protein tyrosine kinase activator activity / vascular endothelial growth factor receptor 2 binding / positive regulation of vascular permeability / commissural neuron axon guidance / dopaminergic neuron differentiation / tube formation / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of blood vessel branching / platelet-derived growth factor receptor binding / surfactant homeostasis / retinal ganglion cell axon guidance / sprouting angiogenesis / cell migration involved in sprouting angiogenesis / extracellular matrix binding / endothelial cell proliferation / epithelial cell maturation / positive regulation of leukocyte migration / positive regulation of positive chemotaxis / cardiac muscle cell development / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of endothelial cell chemotaxis / positive regulation of cell migration involved in sprouting angiogenesis / vascular endothelial growth factor signaling pathway / artery morphogenesis / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of DNA biosynthetic process / negative regulation of epithelial to mesenchymal transition / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / negative regulation of fat cell differentiation / positive chemotaxis / chemoattractant activity / positive regulation of sprouting angiogenesis / positive regulation of protein autophosphorylation / mesoderm development / outflow tract morphogenesis / monocyte differentiation / fibronectin binding / positive regulation of cell division / positive regulation of receptor internalization / macrophage differentiation / cellular response to vascular endothelial growth factor stimulus / mammary gland alveolus development / neuroblast proliferation / positive regulation of focal adhesion assembly / positive regulation of blood vessel endothelial cell migration / vascular endothelial growth factor receptor signaling pathway / positive regulation of osteoblast differentiation / heart morphogenesis / vasculogenesis / cell maturation / ovarian follicle development / lactation / positive regulation of endothelial cell proliferation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / epithelial cell differentiation / extracellular matrix / homeostasis of number of cells within a tissue
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 ...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 / Immunoglobulin FC, subunit C / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ribbon / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsMurray, J.M. / Wiesmann, C.
CitationJournal: Chem.Biol. / Year: 2011
Title: The development of Peptide-based tools for the analysis of angiogenesis.
Authors: Fedorova, A. / Zobel, K. / Gill, H.S. / Ogasawara, A. / Flores, J.E. / Tinianow, J.N. / Vanderbilt, A.N. / Wu, P. / Meng, Y.G. / Williams, S.P. / Wiesmann, C. / Murray, J. / Marik, J. / Deshayes, K.
History
DepositionMay 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Z-domain
B: Z-domain
V: Vascular endothelial growth factor A
W: Vascular endothelial growth factor A


Theoretical massNumber of molelcules
Total (without water)37,2424
Polymers37,2424
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-47 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.228, 72.760, 76.344
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Z-domain


Mass: 6672.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Fmoc solid-phase peptide synthesis
#2: Protein Vascular endothelial growth factor A / VEGF-A / Vascular permeability factor / VPF


Mass: 11948.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: vegf / Production host: Escherichia coli (E. coli) / References: UniProt: P15692
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M KI, 0.1 M MES, PEG 4000 25.0% v/v, pH 6.5, vapor diffusion, hanging drop, temperature 289K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2008
RadiationProtocol: SINGLE / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→52.706 Å / Num. all: 14337 / Num. obs: 14337 / % possible obs: 91.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.534.90.5571.41101822300.557100
2.53-2.684.90.4671.7842417080.46780.1
2.68-2.874.90.282.7939719210.2895.9
2.87-3.14.80.1794.2902018600.17999.8
3.1-3.394.80.1066.6819517100.10699.8
3.39-3.794.80.0798.2524110970.07969.4
3.79-4.384.60.05710.5530911620.05783.1
4.38-5.374.20.04413.2483811490.04496.3
5.37-7.594.80.0698.445669420.06999.3
7.59-52.7064.60.03115.625395580.03198.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALA3.2.25data scaling
PHASERphasing
PHENIXdev_751refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→41.918 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7681 / SU ML: 0.7 / σ(F): 1.39 / Phase error: 28.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.271 632 4.87 %Random
Rwork0.2266 ---
obs0.2288 12982 99.23 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.967 Å2 / ksol: 0.311 e/Å3
Displacement parametersBiso max: 152.2 Å2 / Biso mean: 56.9583 Å2 / Biso min: 17.84 Å2
Baniso -1Baniso -2Baniso -3
1--9.0168 Å20 Å20 Å2
2--7.6865 Å2-0 Å2
3---1.3303 Å2
Refinement stepCycle: LAST / Resolution: 2.55→41.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 0 37 2379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042404
X-RAY DIFFRACTIONf_angle_d0.7853241
X-RAY DIFFRACTIONf_chiral_restr0.053346
X-RAY DIFFRACTIONf_plane_restr0.004431
X-RAY DIFFRACTIONf_dihedral_angle_d17.443911
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5501-2.7470.33991280.31812412254099
2.747-3.02340.36871100.287824612571100
3.0234-3.46070.32821260.252524622588100
3.4607-4.35930.26321240.20862432255698
4.3593-41.92320.21441440.186825832727100
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)
13.21562.4133-0.69974.10310.4053.49040.4567-0.1322-0.7571-0.0559-0.5755-0.17690.85440.4634-0.33871.24820.11350.19580.1921-0.10110.5348-11.2979-38.5589-7.493
27.07420.7901-0.78364.37491.30974.13740.1869-0.7936-0.7620.5362-0.4935-0.06441.62930.2646-0.10051.07540.05410.15310.34410.01910.697-14.9533-37.6831.729
36.56871.00320.74734.76540.61254.2825-0.19050.5485-1.50050.08580.122-0.21181.06810.4817-0.21381.57510.1430.16980.38880.03230.7974-13.233-46.9787-3.6233
44.125-2.4752-1.18735.75240.19092.3226-0.1446-0.02090.3236-0.2581-0.0039-0.4041-0.020.2052-0.05620.4408-0.0677-0.0020.1661-0.0030.2201-12.77179.08318.9883
56.153-1.5620.08975.12871.75233.820.3976-0.58390.3372-0.67320.1782-0.3263-0.0706-0.3762-0.08560.653-0.08470.01690.27510.02570.2186-12.28768.54989.0301
65.4575-1.8218-0.15684.17140.60313.38040.21660.07610.6313-0.236-0.0202-0.3572-0.63530.1664-0.26920.6562-0.05960.13490.18130.05810.3945-10.871517.520215.3876
72.08960.27340.4422.13392.67776.4502-0.1716-0.1678-0.1862-0.07720.2061-0.0813-0.0993-0.11120.08340.4277-0.0196-0.01480.15810.0350.227-17.4804-8.60346.0645
84.14423.01691.81332.41160.76642.1982-0.11481.1124-1.5279-1.7435-0.02181.29651.1644-0.1362-0.33881.1111-0.0301-0.4276-0.1504-0.09680.9819-28.3557-25.0762-15.3196
91.5315-0.26521.23615.85210.44624.26580.0346-0.1545-0.1364-0.22060.03610.09860.0734-1.12880.11240.511-0.11660.10860.19810.13440.1776-21.468-12.5731-1.7789
101.7197-0.91770.24523.9529-0.86363.0473-0.02670.6972-0.4002-0.7144-0.08080.16120.0613-0.17090.10660.55690.01320.01160.20060.14290.038-17.685-14.3148-9.3731
113.298-1.29380.72784.9518-0.41084.73530.2210.3041-0.574-0.4167-0.10090.19190.7215-0.0705-0.00980.4978-0.04380.03950.36080.05570.2415-19.8212-17.4925-10.3621
120.3941-0.8709-1.19592.95072.47394.41830.011-0.072-0.45620.2314-0.31190.08020.61830.06040.28070.64090.0060.0610.18860.01210.4034-18.2667-19.86363.4202
134.101-1.2482-0.5653.6795-1.14440.6129-0.7636-1.46810.58990.9605-0.61781.22690.0141-1.13430.41290.54020.0986-0.15490.4143-0.10860.5429-34.244-1.255517.8129
140.658-1.6454-1.03365.79523.04653.6663-0.11960.1305-0.35250.2793-0.55460.57480.9227-0.61940.38990.6915-0.17610.10760.22060.02680.2778-24.2203-15.74978.2828
150.48230.6455-0.11326.113.15172.66120.14340.0407-0.25011.3629-0.6280.00571.1763-0.3530.40890.7546-0.09890.04860.19190.02660.268-23.3187-12.376917.6445
161.34610.48280.43943.52214.0534.433-0.6459-0.9253-0.5255-0.3784-0.71120.55170.7567-0.379-0.01420.6157-0.2270.01940.21670.1454-0.1322-25.099-9.132517.5058
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 6:23)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 24:37)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 38:57)A0
4X-RAY DIFFRACTION4chain 'B' and (resseq 6:23)B0
5X-RAY DIFFRACTION5chain 'B' and (resseq 24:37)B0
6X-RAY DIFFRACTION6chain 'B' and (resseq 38:57)B0
7X-RAY DIFFRACTION7chain 'V' and (resseq 13:38)V0
8X-RAY DIFFRACTION8chain 'V' and (resseq 39:45)V0
9X-RAY DIFFRACTION9chain 'V' and (resseq 46:65)V0
10X-RAY DIFFRACTION10chain 'V' and (resseq 66:83)V0
11X-RAY DIFFRACTION11chain 'V' and (resseq 84:107)V0
12X-RAY DIFFRACTION12chain 'W' and (resseq 14:38)W0
13X-RAY DIFFRACTION13chain 'W' and (resseq 39:45)W0
14X-RAY DIFFRACTION14chain 'W' and (resseq 46:66)W0
15X-RAY DIFFRACTION15chain 'W' and (resseq 67:83)W0
16X-RAY DIFFRACTION16chain 'W' and (resseq 84:106)W0

+
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