[English] 日本語
Yorodumi
- PDB-3mjk: Structure of a growth factor precursor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mjk
TitleStructure of a growth factor precursor
ComponentsPlatelet-derived growth factor subunit A
KeywordsHORMONE / cystine-knot / growth factor
Function / homology
Function and homology information


regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling / embryonic lung development / negative regulation of phosphatidylinositol biosynthetic process / platelet-derived growth factor complex / platelet-derived growth factor receptor-alpha signaling pathway / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / platelet-derived growth factor receptor-ligand complex / platelet-derived growth factor binding / Signaling by PDGF / cell activation ...regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling / embryonic lung development / negative regulation of phosphatidylinositol biosynthetic process / platelet-derived growth factor complex / platelet-derived growth factor receptor-alpha signaling pathway / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / platelet-derived growth factor receptor-ligand complex / platelet-derived growth factor binding / Signaling by PDGF / cell activation / cell projection assembly / regulation of smooth muscle cell migration / platelet-derived growth factor receptor binding / digestive tract development / positive regulation of mesenchymal cell proliferation / regulation of peptidyl-tyrosine phosphorylation / NFE2L2 regulating tumorigenic genes / negative chemotaxis / skin development / lung alveolus development / positive regulation of protein autophosphorylation / microvillus / platelet-derived growth factor receptor signaling pathway / positive regulation of cell division / Non-integrin membrane-ECM interactions / negative regulation of platelet activation / hair follicle development / collagen binding / positive regulation of MAP kinase activity / Downstream signal transduction / platelet alpha granule lumen / animal organ morphogenesis / regulation of actin cytoskeleton organization / growth factor activity / wound healing / bone development / response to wounding / Golgi lumen / positive regulation of fibroblast proliferation / Constitutive Signaling by Aberrant PI3K in Cancer / Platelet degranulation / cell-cell signaling / PIP3 activates AKT signaling / actin cytoskeleton organization / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / angiogenesis / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / positive regulation of cell migration / endoplasmic reticulum lumen / protein heterodimerization activity / Golgi membrane / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Platelet-derived growth factor, N-terminal / Platelet-derived growth factor, N terminal region / 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 Cytokines, subunit B / Cystine-knot cytokines ...Platelet-derived growth factor, N-terminal / Platelet-derived growth factor, N terminal region / 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 Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Platelet-derived growth factor subunit A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLiu, H. / He, X.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structures of a platelet-derived growth factor/propeptide complex and a platelet-derived growth factor/receptor complex.
Authors: Shim, A.H. / Liu, H. / Focia, P.J. / Chen, X. / Lin, P.C. / He, X.
History
DepositionApr 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Platelet-derived growth factor subunit A
B: Platelet-derived growth factor subunit A
E: Platelet-derived growth factor subunit A
F: Platelet-derived growth factor subunit A
X: Platelet-derived growth factor subunit A
Y: Platelet-derived growth factor subunit A


Theoretical massNumber of molelcules
Total (without water)116,4026
Polymers116,4026
Non-polymers00
Water13,637757
1
A: Platelet-derived growth factor subunit A
B: Platelet-derived growth factor subunit A


Theoretical massNumber of molelcules
Total (without water)38,8012
Polymers38,8012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-40 kcal/mol
Surface area15210 Å2
MethodPISA
2
E: Platelet-derived growth factor subunit A
F: Platelet-derived growth factor subunit A


Theoretical massNumber of molelcules
Total (without water)38,8012
Polymers38,8012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-44 kcal/mol
Surface area14630 Å2
MethodPISA
3
X: Platelet-derived growth factor subunit A
Y: Platelet-derived growth factor subunit A


Theoretical massNumber of molelcules
Total (without water)38,8012
Polymers38,8012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-41 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.841, 119.208, 146.712
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Platelet-derived growth factor subunit A / PDGF subunit A / Platelet-derived growth factor A chain / Platelet-derived growth factor alpha ...PDGF subunit A / Platelet-derived growth factor A chain / Platelet-derived growth factor alpha polypeptide / PDGF-1


Mass: 19400.377 Da / Num. of mol.: 6 / Fragment: UNP residues 21-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDGF1, PDGFA / Plasmid: pVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: P04085
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 757 / 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: 1.9 Å3/Da / Density % sol: 35.3 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.0 M sodium citrate, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9786 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 14, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 46182 / Num. obs: 45306 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.074 / Net I/σ(I): 15.6
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5661 / Rsym value: 0.566 / % possible all: 95.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry: 1PDG

1pdg


Resolution: 2.4→48.04 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2735506.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1782 5.1 %RANDOM
Rwork0.225 ---
obs0.225 35193 98.6 %-
all-35692 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.3119 Å2 / ksol: 0.293525 e/Å3
Displacement parametersBiso mean: 65.5 Å2
Baniso -1Baniso -2Baniso -3
1-11.96 Å20 Å20 Å2
2---9.22 Å20 Å2
3----2.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.4→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5975 0 0 757 6732
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_mcbond_it5.961.5
X-RAY DIFFRACTIONc_mcangle_it10.332
X-RAY DIFFRACTIONc_scbond_it8.382
X-RAY DIFFRACTIONc_scangle_it13.712.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.389 321 5.6 %
Rwork0.385 5384 -
obs-5705 97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION4ion.param

+
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