[English] 日本語
Yorodumi
- PDB-7ppa: High resolution structure of bone morphogenetic protein receptor ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ppa
TitleHigh resolution structure of bone morphogenetic protein receptor type II (BMPRII) extracellular domain in complex with BMP10
Components
  • Bone morphogenetic protein 10
  • Bone morphogenetic protein receptor type-2
KeywordsCYTOKINE / BMPRII BMP10 TGF-beta ligand and receptor Signalling complex
Function / homology
Function and homology information


semi-lunar valve development / atrial cardiac muscle tissue morphogenesis / regulation of cardiac muscle hypertrophy in response to stress / activin receptor activity, type II / negative regulation of chondrocyte proliferation / lymphatic endothelial cell differentiation / regulation of lung blood pressure / pulmonary valve development / tricuspid valve morphogenesis / positive regulation of cell proliferation involved in heart morphogenesis ...semi-lunar valve development / atrial cardiac muscle tissue morphogenesis / regulation of cardiac muscle hypertrophy in response to stress / activin receptor activity, type II / negative regulation of chondrocyte proliferation / lymphatic endothelial cell differentiation / regulation of lung blood pressure / pulmonary valve development / tricuspid valve morphogenesis / positive regulation of cell proliferation involved in heart morphogenesis / chondrocyte development / positive regulation of sarcomere organization / venous blood vessel development / negative regulation of cell proliferation involved in heart valve morphogenesis / aortic valve development / ventricular cardiac muscle cell development / BMP binding / negative regulation of muscle cell differentiation / proteoglycan biosynthetic process / atrial septum morphogenesis / endocardial cushion development / positive regulation of cartilage development / maternal placenta development / endochondral bone morphogenesis / telethonin binding / transforming growth factor beta receptor activity / lung vasculature development / lymphangiogenesis / mitral valve morphogenesis / retina vasculature development in camera-type eye / BMP receptor activity / negative regulation of cardiac muscle hypertrophy / positive regulation of axon extension involved in axon guidance / artery development / receptor protein serine/threonine kinase / cellular response to BMP stimulus / Signaling by BMP / activin receptor signaling pathway / endothelial cell apoptotic process / receptor serine/threonine kinase binding / adult heart development / heart trabecula formation / positive regulation of ossification / negative regulation of systemic arterial blood pressure / limb development / endothelial cell proliferation / negative regulation of endothelial cell migration / Molecules associated with elastic fibres / anterior/posterior pattern specification / ventricular cardiac muscle tissue morphogenesis / cardiac muscle cell proliferation / cell surface receptor protein serine/threonine kinase signaling pathway / negative regulation of vasoconstriction / sarcomere organization / ventricular septum morphogenesis / lung alveolus development / positive regulation of epithelial cell migration / blood vessel development / positive regulation of cardiac muscle hypertrophy / growth factor binding / outflow tract morphogenesis / positive regulation of SMAD protein signal transduction / mesoderm formation / regulation of cardiac muscle contraction / blood vessel remodeling / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / clathrin-coated pit / positive regulation of cardiac muscle cell proliferation / cellular response to starvation / basal plasma membrane / protein tyrosine kinase binding / negative regulation of cell migration / kidney development / cytokine activity / adherens junction / negative regulation of smooth muscle cell proliferation / growth factor activity / negative regulation of cell growth / hormone activity / caveola / cellular response to growth factor stimulus / Z disc / osteoblast differentiation / regulation of cell population proliferation / postsynaptic density / receptor complex / cell adhesion / cadherin binding / apical plasma membrane / axon / neuronal cell body / dendrite / positive regulation of gene expression / positive regulation of DNA-templated transcription / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain ...TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / Snake toxin-like superfamily / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Bone morphogenetic protein 10 / Bone morphogenetic protein receptor type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsGuo, J. / Yu, M. / Read, R.J. / 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 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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 1.2Nov 6, 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: Bone morphogenetic protein 10
B: Bone morphogenetic protein 10
C: Bone morphogenetic protein receptor type-2
D: Bone morphogenetic protein receptor type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3775
Polymers52,2854
Non-polymers921
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-48 kcal/mol
Surface area21660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.718, 47.228, 250.085
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32C
42D

NCS domain segments:

Beg auth comp-ID: ASN / Beg label comp-ID: ASN

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111CYSCYSAA321 - 4235 - 107
221CYSCYSBB321 - 4235 - 107
332PROPROCC29 - 1334 - 108
442LEULEUDD29 - 1394 - 114

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

-
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 receptor type-2 / BMP type-2 receptor / BMPR-2 / Bone morphogenetic protein receptor type II / BMP type II receptor / BMPR-II


Mass: 13965.368 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMPR2, PPH1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13873, receptor protein serine/threonine kinase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.54 Å3/Da / Density % sol: 51.63 % / Description: Thick plate
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 14% PEG 3350 0.19 M Ammonium citrate dibasic 0.02 M Sodium citrate tribasic dihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91589 Å
DetectorType: DECTRIS EIGER2 XE 16M / 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: 1.48→125.04 Å / Num. obs: 89787 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.032 / Rrim(I) all: 0.115 / Net I/σ(I): 11.2
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.85 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4320 / CC1/2: 0.59 / Rpim(I) all: 0.554 / Rrim(I) all: 1.933 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
DIALS1.14.5data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SF3, 2HLQ

6sf3

2hlq


Resolution: 1.48→125.04 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.66 / SU ML: 0.05 / Cross valid method: FREE R-VALUE / ESU R: 0.062 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2066 4383 4.889 %
Rwork0.1646 85272 -
all0.167 --
obs-89655 99.886 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.737 Å2
Baniso -1Baniso -2Baniso -3
1--0.651 Å20 Å20 Å2
2---0.492 Å20 Å2
3---1.143 Å2
Refinement stepCycle: LAST / Resolution: 1.48→125.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 6 352 3523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0133404
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173055
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.6514655
X-RAY DIFFRACTIONr_angle_other_deg1.5481.587117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2145437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.47623.379145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87415546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8141511
X-RAY DIFFRACTIONr_chiral_restr0.1070.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024414
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02737
X-RAY DIFFRACTIONr_nbd_refined0.2290.2630
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.22709
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21606
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21575
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.090.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2240.228
X-RAY DIFFRACTIONr_nbd_other0.2040.298
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2690.231
X-RAY DIFFRACTIONr_mcbond_it7.1943.3181718
X-RAY DIFFRACTIONr_mcbond_other7.1963.3151717
X-RAY DIFFRACTIONr_mcangle_it7.6814.932159
X-RAY DIFFRACTIONr_mcangle_other7.684.9342160
X-RAY DIFFRACTIONr_scbond_it10.3513.7391686
X-RAY DIFFRACTIONr_scbond_other10.3483.7411687
X-RAY DIFFRACTIONr_scangle_it10.4525.42494
X-RAY DIFFRACTIONr_scangle_other10.455.4022495
X-RAY DIFFRACTIONr_lrange_it9.7431.8023813
X-RAY DIFFRACTIONr_lrange_other9.7219125.3873727
X-RAY DIFFRACTIONr_rigid_bond_restr15.34232687
X-RAY DIFFRACTIONr_ncsr_local_group_10.1210.053208
X-RAY DIFFRACTIONr_ncsr_local_group_20.1830.052563
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.121230.05007
12BX-RAY DIFFRACTIONLocal ncs0.121230.05007
23CX-RAY DIFFRACTIONLocal ncs0.182930.05007
24DX-RAY DIFFRACTIONLocal ncs0.182930.05007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.5180.3013450.2616144X-RAY DIFFRACTION99.6774
1.518-1.560.2793370.256027X-RAY DIFFRACTION99.8275
1.56-1.6050.2623070.215904X-RAY DIFFRACTION99.8874
1.605-1.6550.222860.1815758X-RAY DIFFRACTION99.9835
1.655-1.7090.2572610.1755599X-RAY DIFFRACTION99.9659
1.709-1.7690.2212650.1645372X-RAY DIFFRACTION99.876
1.769-1.8360.2062660.1485183X-RAY DIFFRACTION99.9633
1.836-1.9110.1782840.1285040X-RAY DIFFRACTION99.9812
1.911-1.9960.1952310.1434810X-RAY DIFFRACTION99.9009
1.996-2.0930.1972440.1554626X-RAY DIFFRACTION100
2.093-2.2060.1951990.1574416X-RAY DIFFRACTION99.9783
2.206-2.340.1952170.1514197X-RAY DIFFRACTION99.9773
2.34-2.5020.1922320.1553933X-RAY DIFFRACTION99.952
2.502-2.7020.2161870.1693642X-RAY DIFFRACTION99.9217
2.702-2.960.2031750.1593447X-RAY DIFFRACTION99.8897
2.96-3.3090.1881500.1573063X-RAY DIFFRACTION99.9689
3.309-3.8210.1831340.1452767X-RAY DIFFRACTION99.8967
3.821-4.6790.1781090.1292368X-RAY DIFFRACTION99.9596
4.679-6.6160.2151010.1911865X-RAY DIFFRACTION100
6.616-125.040.275530.2681111X-RAY DIFFRACTION99.8285

+
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