[English] 日本語
Yorodumi
- PDB-7poi: Prodomain bound BMP10 crystal form 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7poi
TitleProdomain bound BMP10 crystal form 1
Components(Bone morphogenetic protein 10) x 2
KeywordsCYTOKINE / BMP10 bone morphogenetic protein prodomain TGFbeta signalling
Function / homology
Function and homology information


atrial cardiac muscle tissue morphogenesis / regulation of cardiac muscle hypertrophy in response to stress / positive regulation of cell proliferation involved in heart morphogenesis / positive regulation of sarcomere organization / ventricular cardiac muscle cell development / positive regulation of cartilage development / telethonin binding / negative regulation of cardiac muscle hypertrophy / Signaling by BMP / activin receptor signaling pathway ...atrial cardiac muscle tissue morphogenesis / regulation of cardiac muscle hypertrophy in response to stress / positive regulation of cell proliferation involved in heart morphogenesis / positive regulation of sarcomere organization / ventricular cardiac muscle cell development / positive regulation of cartilage development / telethonin binding / negative regulation of cardiac muscle hypertrophy / Signaling by BMP / activin receptor signaling pathway / heart trabecula formation / receptor serine/threonine kinase binding / adult heart development / Molecules associated with elastic fibres / negative regulation of endothelial cell migration / cardiac muscle cell proliferation / ventricular cardiac muscle tissue morphogenesis / sarcomere organization / positive regulation of cardiac muscle hypertrophy / positive regulation of SMAD protein signal transduction / regulation of cardiac muscle contraction / BMP signaling pathway / positive regulation of cardiac muscle cell proliferation / negative regulation of cell migration / kidney development / cytokine activity / growth factor activity / negative regulation of cell growth / hormone activity / Z disc / cell adhesion / positive regulation of gene expression / positive regulation of DNA-templated transcription / cell surface / extracellular space / extracellular region / cytoplasm
Similarity search - Function
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. / Cystine-knot cytokine
Similarity search - Domain/homology
D(-)-TARTARIC ACID / Bone morphogenetic protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGuo, J. / Yu, M. / Li, W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationPG/12/54/29734, PG/17/1/32532, FS/SBSRF/20/31005 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Crystal structures of BMPRII extracellular domain in binary and ternary receptor complexes with BMP10.
Authors: Guo, J. / Liu, B. / Thorikay, M. / Yu, M. / Li, X. / Tong, Z. / Salmon, R.M. / Read, R.J. / Ten Dijke, P. / Morrell, N.W. / Li, W.
History
DepositionSep 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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
A: Bone morphogenetic protein 10
B: Bone morphogenetic protein 10
C: Bone morphogenetic protein 10
D: Bone morphogenetic protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5747
Polymers91,9814
Non-polymers5933
Water19811
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.897, 214.041, 106.967
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_1ens_2(chain "C" and (resid 81 through 117 or resid 126 through 172 or resid 181 through 301))
d_2ens_2(chain "D" and (resid 81 through 148 or resid 162 through 260 or resid 301))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNARGA1 - 104
d_21ens_1ASNARGB1 - 104
d_11ens_2PROPROC3 - 39
d_12ens_2TYRGLUC48 - 81
d_13ens_2ARGGLNC84 - 143
d_14ens_2NAGNAGD
d_21ens_2PROTYRE1 - 60
d_22ens_2ASPGLNE63 - 133
d_23ens_2NAGNAGF

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.53269060942, 0.00318576476634, 0.846304062107), (0.00226507900262, -0.999983966641, 0.00518997863626), (0.846307027061, 0.00468159844354, 0.532674852592)-22.8123402897, -44.5767211435, 12.7779660165
2given(-0.547770919491, -0.00606310654876, 0.83660639401), (0.0569261657489, -0.997926343931, 0.0300403685464), (0.834689422128, 0.0640800345525, 0.546980180408)-23.0261030136, -44.9111217018, 15.4161478942

-
Components

#1: Protein Bone morphogenetic protein 10 / / BMP-10


Mass: 12177.185 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP10 / Cell line (production host): HEK EBNA / Production host: Homo sapiens (human) / References: UniProt: O95393
#2: Protein Bone morphogenetic protein 10 / / BMP-10


Mass: 33813.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP10 / Cell line (production host): HEK EBNA / Production host: Homo sapiens (human) / References: UniProt: O95393
#3: Chemical ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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 / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 19% PEG 3350 0.15 M Ammonium tartrate dibasic 0.02 M Sodium cacodylate trihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91589 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91589 Å / Relative weight: 1
ReflectionResolution: 2.9→107.02 Å / Num. obs: 19024 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 91.59 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.048 / Rrim(I) all: 0.173 / Net I/σ(I): 10.1
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 12.8 % / Rmerge(I) obs: 3.761 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3033 / CC1/2: 0.482 / Rpim(I) all: 1.094 / Rrim(I) all: 3.919 / % possible all: 100

-
Processing

Software
NameVersionClassification
DIALS1.14.5data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SF3, 4YCI

6sf3

4yci


Resolution: 2.9→107.02 Å / SU ML: 0.5248 / Cross valid method: FREE R-VALUE / σ(F): 0.34 / Phase error: 34.0263
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2684 968 5.1 %
Rwork0.2185 33990 -
obs0.2209 18998 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 112.09 Å2
Refinement stepCycle: LAST / Resolution: 2.9→107.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3929 0 38 11 3978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224060
X-RAY DIFFRACTIONf_angle_d0.47015497
X-RAY DIFFRACTIONf_chiral_restr0.0433611
X-RAY DIFFRACTIONf_plane_restr0.004693
X-RAY DIFFRACTIONf_dihedral_angle_d14.94621508
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.542279018527
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS1.65146226248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.980.40541020.38122674X-RAY DIFFRACTION99.82
2.98-3.070.40881520.36542616X-RAY DIFFRACTION99.64
3.07-3.170.4341370.34682614X-RAY DIFFRACTION99.78
3.17-3.280.34571340.29212572X-RAY DIFFRACTION99.85
3.28-3.410.33511450.27862635X-RAY DIFFRACTION99.89
3.41-3.560.33071350.25212593X-RAY DIFFRACTION99.78
3.56-3.750.25351330.24582624X-RAY DIFFRACTION99.89
3.75-3.990.2431610.2232614X-RAY DIFFRACTION99.93
3.99-4.30.25711420.19292608X-RAY DIFFRACTION100
4.3-4.730.24421300.16332629X-RAY DIFFRACTION100
4.73-5.410.22371840.18022575X-RAY DIFFRACTION100
5.41-6.820.30451390.22072624X-RAY DIFFRACTION100
6.82-107.020.22671330.1942612X-RAY DIFFRACTION99.35
Refinement TLS params.Method: refined / Origin x: -3.41330751624 Å / Origin y: -22.6833408638 Å / Origin z: 19.663638474 Å
111213212223313233
T0.655657993381 Å2-0.198930489185 Å20.0836183497324 Å2-0.852948447634 Å2-0.0176319589254 Å2--0.282100839355 Å2
L1.59637506289 °2-1.0033141669 °20.481405644894 °2-2.68730779016 °2-0.01366447971 °2--1.19896380519 °2
S0.144186284875 Å °0.0437807030335 Å °-0.0430720823357 Å °-0.167418253086 Å °-0.14072786243 Å °0.164620085901 Å °-0.283708133718 Å °-0.0483472096635 Å °0.0354416130738 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