[English] 日本語
Yorodumi
- PDB-6sf2: Ternary complex of human bone morphogenetic protein 9 (BMP9) grow... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sf2
TitleTernary complex of human bone morphogenetic protein 9 (BMP9) growth factor domain, its prodomain and extracellular domain of activin receptor-like kinase 1 (ALK1).
Components
  • (Growth/differentiation factor 2) x 2
  • Serine/threonine-protein kinase receptor R3
KeywordsCYTOKINE / BMP9 / ALK1 / prodomain / ternary complex / signalling / TGFbeta / BMP
Function / homology
Function and homology information


lymphatic endothelial cell differentiation / regulation of endothelial cell proliferation / negative regulation of endothelial cell differentiation / dorsal aorta morphogenesis / blood vessel maturation / positive regulation of epithelial cell differentiation / venous blood vessel development / positive regulation of cartilage development / transforming growth factor beta receptor activity / positive regulation of chondrocyte differentiation ...lymphatic endothelial cell differentiation / regulation of endothelial cell proliferation / negative regulation of endothelial cell differentiation / dorsal aorta morphogenesis / blood vessel maturation / positive regulation of epithelial cell differentiation / venous blood vessel development / positive regulation of cartilage development / transforming growth factor beta receptor activity / positive regulation of chondrocyte differentiation / lymphangiogenesis / BMP receptor complex / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / BMP receptor activity / endothelial tube morphogenesis / retina vasculature development in camera-type eye / positive regulation of endothelial cell differentiation / transforming growth factor beta receptor activity, type I / negative regulation of focal adhesion assembly / regulation of blood vessel endothelial cell migration / activin receptor activity, type I / artery development / transmembrane receptor protein serine/threonine kinase activity / receptor protein serine/threonine kinase / activin binding / cellular response to BMP stimulus / Signaling by BMP / activin receptor signaling pathway / positive regulation of bicellular tight junction assembly / positive regulation of BMP signaling pathway / negative regulation of cell adhesion / dorsal/ventral pattern formation / transforming growth factor beta binding / cartilage development / blood vessel morphogenesis / negative regulation of endothelial cell migration / blood circulation / wound healing, spreading of epidermal cells / endocardial cushion morphogenesis / branching involved in blood vessel morphogenesis / positive regulation of Notch signaling pathway / negative regulation of DNA replication / SMAD binding / negative regulation of endothelial cell proliferation / regulation of DNA replication / negative regulation of blood vessel endothelial cell migration / positive regulation of SMAD protein signal transduction / blood vessel remodeling / BMP signaling pathway / cellular response to transforming growth factor beta stimulus / vasculogenesis / positive regulation of endothelial cell proliferation / transforming growth factor beta receptor signaling pathway / ossification / negative regulation of cell migration / negative regulation of angiogenesis / protein serine/threonine kinase activator activity / cytokine activity / positive regulation of interleukin-8 production / growth factor activity / negative regulation of cell growth / cellular response to growth factor stimulus / regulation of blood pressure / positive regulation of angiogenesis / osteoblast differentiation / heart development / angiogenesis / in utero embryonic development / intracellular iron ion homeostasis / transcription by RNA polymerase II / cell differentiation / negative regulation of cell population proliferation / negative regulation of gene expression / protein serine/threonine kinase activity / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family ...GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / Snake toxin-like superfamily / Ribbon / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Activin receptor type-1-like / Growth/differentiation factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsSalmon, R.M. / Guo, J. / Yu, M. / Li, W.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
British Heart FoundationPG/12/54/29734 United Kingdom
British Heart FoundationPG/15/39/31519 United Kingdom
British Heart FoundationPG/17/1/32532 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Molecular basis of ALK1-mediated signalling by BMP9/BMP10 and their prodomain-bound forms.
Authors: Salmon, R.M. / Guo, J. / Wood, J.H. / Tong, Z. / Beech, J.S. / Lawera, A. / Yu, M. / Grainger, D.J. / Reckless, J. / Morrell, N.W. / Li, W.
History
DepositionJul 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase receptor R3
B: Growth/differentiation factor 2
C: Growth/differentiation factor 2
D: Serine/threonine-protein kinase receptor R3
E: Growth/differentiation factor 2
F: Growth/differentiation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,4348
Polymers111,9926
Non-polymers4422
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9260 Å2
ΔGint-66 kcal/mol
Surface area30310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.610, 72.610, 438.485
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROLEULEU(chain 'A' and (resid 30 through 60 or (resid 61...AA30 - 10310 - 83
221PROPROLEULEU(chain 'D' and (resid 30 through 36 or (resid 37...DD30 - 10310 - 83
132SERSERLYSLYS(chain 'B' and (resid 325 through 336 or (resid 337...BB325 - 3906 - 71
142CYSCYSARGARG(chain 'B' and (resid 325 through 336 or (resid 337...BB393 - 42974 - 110
252SERSERLYSLYS(chain 'E' and ((resid 325 and (name N or name...EE325 - 3906 - 71
262CYSCYSARGARG(chain 'E' and ((resid 325 and (name N or name...EE393 - 42974 - 110

NCS ensembles :
ID
1
2

-
Components

#1: Protein Serine/threonine-protein kinase receptor R3 / SKR3 / Activin receptor-like kinase 1 / ALK-1 / TGF-B superfamily receptor type I / TSR-I


Mass: 10788.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVRL1, ACVRLK1, ALK1 / Production host: Escherichia coli (E. coli)
References: UniProt: P37023, receptor protein serine/threonine kinase
#2: Protein Growth/differentiation factor 2 / GDF-2 / Bone morphogenetic protein 9 / BMP-9


Mass: 12102.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDF2, BMP9 / Cell line (production host): HEK-EBNA / Production host: Homo sapiens (human) / References: UniProt: Q9UK05
#3: Protein Growth/differentiation factor 2 / GDF-2 / Bone morphogenetic protein 9 / BMP-9


Mass: 33104.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDF2, BMP9 / Cell line (production host): HEK-EBNA / Production host: Homo sapiens (human) / References: UniProt: Q9UK05
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.14 M potassium sodium tartrate, 14% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 3.3→62.88 Å / Num. obs: 19622 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 90.13 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.052 / Rrim(I) all: 0.163 / Net I/σ(I): 13.3
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2834 / CC1/2: 0.779 / Rpim(I) all: 0.369 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FAO, 4YCG

4fao

4ycg


Resolution: 3.3→62.25 Å / SU ML: 0.4924 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.5581
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2743 996 5.1 %
Rwork0.2426 18522 -
obs0.2441 19518 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.58 Å2
Refinement stepCycle: LAST / Resolution: 3.3→62.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4347 0 28 9 4384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00184488
X-RAY DIFFRACTIONf_angle_d0.48966136
X-RAY DIFFRACTIONf_chiral_restr0.0422718
X-RAY DIFFRACTIONf_plane_restr0.0033787
X-RAY DIFFRACTIONf_dihedral_angle_d10.9589634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.470.34471500.30752625X-RAY DIFFRACTION99.93
3.47-3.690.32781460.28332635X-RAY DIFFRACTION99.89
3.69-3.980.2881500.26772623X-RAY DIFFRACTION99.96
3.98-4.380.25411330.22312657X-RAY DIFFRACTION99.96
4.38-5.010.21771480.20092642X-RAY DIFFRACTION100
5.01-6.310.28371290.24492665X-RAY DIFFRACTION100
6.31-62.250.28181400.24282675X-RAY DIFFRACTION99.89
Refinement TLS params.Method: refined / Origin x: -23.2435955183 Å / Origin y: -20.3457557922 Å / Origin z: -11.4726290322 Å
111213212223313233
T0.58194569458 Å20.150402090821 Å20.0603266094604 Å2-0.621233885191 Å20.0940461379944 Å2--0.746879143477 Å2
L0.433867473125 °20.07605747223 °2-0.538980349733 °2-0.801855628732 °20.390745145245 °2--1.18416219097 °2
S0.0376298875668 Å °-0.116324086007 Å °-0.0289120473988 Å °0.0191895145558 Å °0.0851551448839 Å °0.09561784345 Å °-0.0342887723743 Å °0.0481441147905 Å °-0.122735566358 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