[English] 日本語
Yorodumi
- PDB-5nhr: CRYSTAL STRUCTURE OF THE Activin receptor type-2B LIGAND BINDING ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nhr
TitleCRYSTAL STRUCTURE OF THE Activin receptor type-2B LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV, CUBIC CRYSTAL FORM
Components
  • Activin receptor type-2B
  • Bimagrumab Fv Light-Chain
  • Bimagrumab Fv heavy-chain
KeywordsIMMUNE SYSTEM / three-finger toxin fold / antibody Fv fragment
Function / homology
Function and homology information


Regulation of signaling by NODAL / activin receptor activity / activin receptor activity, type II / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / venous blood vessel development / lymphangiogenesis / trophoblast cell migration / retina vasculature development in camera-type eye / embryonic foregut morphogenesis ...Regulation of signaling by NODAL / activin receptor activity / activin receptor activity, type II / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / venous blood vessel development / lymphangiogenesis / trophoblast cell migration / retina vasculature development in camera-type eye / embryonic foregut morphogenesis / activin receptor complex / artery development / receptor protein serine/threonine kinase / pattern specification process / activin binding / Signaling by BMP / Signaling by Activin / activin receptor signaling pathway / Signaling by NODAL / gastrulation with mouth forming second / pancreas development / kinase activator activity / determination of left/right symmetry / negative regulation of ossification / anterior/posterior pattern specification / negative regulation of cold-induced thermogenesis / cell surface receptor protein serine/threonine kinase signaling pathway / insulin secretion / skeletal system morphogenesis / organ growth / growth factor binding / odontogenesis of dentin-containing tooth / mesoderm development / roof of mouth development / blood vessel remodeling / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / BMP signaling pathway / response to glucose / protein serine/threonine/tyrosine kinase activity / lung development / post-embryonic development / kidney development / cellular response to growth factor stimulus / heart development / intracellular iron ion homeostasis / receptor complex / protein serine/threonine kinase activity / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Activin types I and II receptor domain / Activin types I and II receptor domain / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Ribbon / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Activin types I and II receptor domain / Activin types I and II receptor domain / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Ribbon / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Activin receptor type-2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.35 Å
Model detailsCUBIC CRYSTAL FORM
AuthorsRondeau, J.-M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Blockade of activin type II receptors with a dual anti-ActRIIA/IIB antibody is critical to promote maximal skeletal muscle hypertrophy.
Authors: Morvan, F. / Rondeau, J.-M. / Zou, C. / Minetti, G. / Scheufler, C. / Scharenberg, M. / Jacobi, C. / Brebbia, P. / Ritter, V. / Toussaint, G. / Koelbing, C. / Leber, X. / Schilb, A. / Witte, ...Authors: Morvan, F. / Rondeau, J.-M. / Zou, C. / Minetti, G. / Scheufler, C. / Scharenberg, M. / Jacobi, C. / Brebbia, P. / Ritter, V. / Toussaint, G. / Koelbing, C. / Leber, X. / Schilb, A. / Witte, F. / Lehmann, S. / Koch, E. / Geisse, S. / Glass, D.J. / Lach-Trifilieff, E.
History
DepositionMar 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Bimagrumab Fv Light-Chain
H: Bimagrumab Fv heavy-chain
B: Bimagrumab Fv Light-Chain
A: Bimagrumab Fv heavy-chain
C: Activin receptor type-2B
D: Activin receptor type-2B


Theoretical massNumber of molelcules
Total (without water)75,1696
Polymers75,1696
Non-polymers00
Water00
1
L: Bimagrumab Fv Light-Chain
H: Bimagrumab Fv heavy-chain
C: Activin receptor type-2B


Theoretical massNumber of molelcules
Total (without water)37,5853
Polymers37,5853
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-19 kcal/mol
Surface area14400 Å2
MethodPISA
2
B: Bimagrumab Fv Light-Chain
A: Bimagrumab Fv heavy-chain
D: Activin receptor type-2B


Theoretical massNumber of molelcules
Total (without water)37,5853
Polymers37,5853
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-19 kcal/mol
Surface area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.826, 187.826, 187.826
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23

-
Components

#1: Antibody Bimagrumab Fv Light-Chain


Mass: 12513.700 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING domain
Source method: isolated from a genetically manipulated source
Details: VL domain / Source: (gene. exp.) Homo sapiens (human) / Details (production host): C-terminal Strep tag
Production host: Escherichia coli str. K-12 substr. W3110 (bacteria)
#2: Antibody Bimagrumab Fv heavy-chain


Mass: 13423.935 Da / Num. of mol.: 2 / Fragment: VH
Source method: isolated from a genetically manipulated source
Details: periplasmic expression / Source: (gene. exp.) Homo sapiens (human) / Details (production host): C-terminal His6 tag
Production host: Escherichia coli str. K-12 substr. W3110 (bacteria)
#3: Protein Activin receptor type-2B / Activin receptor type IIB / ACTR-IIB


Mass: 11646.901 Da / Num. of mol.: 2 / Fragment: VL, UNP residues 24-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR2B / Details (production host): Thioredoxin-fusion / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): Shuffle
References: UniProt: Q13705, receptor protein serine/threonine kinase
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 7.35 Å3/Da / Mosaicity: 0.707 ° / Mosaicity esd: 0.003 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6 / Details: 1.4M AMMONIUM SULFATE, 0.1M SODIUM CITRATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→100 Å / Num. obs: 28995 / % possible obs: 90.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.093 / Χ2: 1.066 / Net I/σ(I): 8.2 / Num. measured all: 96966
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
3.35-3.473.20.4820.797193.9
3.47-3.613.20.3320.779193.3
3.61-3.773.30.2550.978192.9
3.77-3.973.30.1830.987192.4
3.97-4.223.40.1211.053191.7
4.22-4.553.40.0881.299191.3
4.55-53.40.0751.274190.2
5-5.733.40.0631.21189.4
5.73-7.223.50.0611.246187.6
7.22-1003.50.0320.994184

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.35 Å45.55 Å
Translation3.35 Å45.55 Å

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASER1.3.1phasing
CNSrefinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H64

2h64


Resolution: 3.35→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.229 1421 4.4 %
Rwork0.2156 --
obs-28995 90.6 %
Displacement parametersBiso max: 112.3 Å2 / Biso mean: 72.1553 Å2 / Biso min: 45.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 3.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4918 0 0 0 4918
Num. residues----636
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d0.942
X-RAY DIFFRACTIONc_mcbond_it1.1811.5
X-RAY DIFFRACTIONc_scbond_it1.5672
X-RAY DIFFRACTIONc_mcangle_it2.0862
X-RAY DIFFRACTIONc_scangle_it2.6212.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramdna-rna.top
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4ion.top

+
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