[English] 日本語
Yorodumi
- PDB-1bte: CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE TYPE II ACTI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bte
TitleCRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE TYPE II ACTIVIN RECEPTOR
ComponentsPROTEIN (ACTIVIN RECEPTOR TYPE II)
KeywordsTRANSFERASE / RECEPTOR / SERINE KINASE / LIGAND BINDING DOMAIN / THREE-FINGER TOXIN
Function / homology
Function and homology information


TGFBR3 regulates activin signaling / Signaling by Activin / inhibin binding / inhibin-betaglycan-ActRII complex / Signaling by BMP / activin receptor activity / penile erection / activin receptor activity, type II / sperm ejaculation / positive regulation of activin receptor signaling pathway ...TGFBR3 regulates activin signaling / Signaling by Activin / inhibin binding / inhibin-betaglycan-ActRII complex / Signaling by BMP / activin receptor activity / penile erection / activin receptor activity, type II / sperm ejaculation / positive regulation of activin receptor signaling pathway / Sertoli cell proliferation / BMP receptor activity / embryonic skeletal system development / activin receptor activity, type I / receptor protein serine/threonine kinase / activin binding / gastrulation with mouth forming second / regulation of nitric oxide biosynthetic process / determination of left/right symmetry / anterior/posterior pattern specification / growth factor binding / odontogenesis of dentin-containing tooth / mesoderm development / positive regulation of SMAD protein signal transduction / regulation of signal transduction / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / coreceptor activity / positive regulation of erythrocyte differentiation / PDZ domain binding / male gonad development / osteoblast differentiation / spermatogenesis / receptor complex / protein serine/threonine kinase activity / cell surface / positive regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / identical protein 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 / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Activin receptor type-2A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.5 Å
AuthorsGreenwald, J. / Fischer, W. / Vale, W. / Choe, S.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Three-finger toxin fold for the extracellular ligand-binding domain of the type II activin receptor serine kinase.
Authors: Greenwald, J. / Fischer, W.H. / Vale, W.W. / Choe, S.
History
DepositionSep 1, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 9, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Dec 11, 2019Group: Advisory / Atomic model / Derived calculations
Category: atom_site / pdbx_struct_assembly ...atom_site / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_symm_contact / struct_conn
Item: _atom_site.occupancy / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 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 / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (ACTIVIN RECEPTOR TYPE II)
B: PROTEIN (ACTIVIN RECEPTOR TYPE II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9006
Polymers23,0162
Non-polymers8854
Water3,639202
1
A: PROTEIN (ACTIVIN RECEPTOR TYPE II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9503
Polymers11,5081
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN (ACTIVIN RECEPTOR TYPE II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9503
Polymers11,5081
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.630, 71.630, 37.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-154-

HOH

21A-156-

HOH

31B-168-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8945, -0.4458, -0.0349), (0.4445, 0.895, -0.0382), (0.0482, 0.0187, 0.9987)
Vector: -19.7137, -37.4157, -14.0347)

-
Components

#1: Protein PROTEIN (ACTIVIN RECEPTOR TYPE II)


Mass: 11507.803 Da / Num. of mol.: 2 / Fragment: LIGAND-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PPIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1168
References: UniProt: P27038, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: 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.: 4
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Compound detailsGLYCOSYLATION FROM HOST EXPRESSION SYSTEM WAS REMOVED USING ENDOGLYCOSIDASE H, LEAVING BEHIND THE N- ...GLYCOSYLATION FROM HOST EXPRESSION SYSTEM WAS REMOVED USING ENDOGLYCOSIDASE H, LEAVING BEHIND THE N-ACETYL GLUCOSAMINE (NAG) RESIDUES ON THE ASN.
Has protein modificationY
Nonpolymer detailsO6 OF NAG A 124 AND NAG B 124 IS MODELED IN TWO ALTERNATIVE CONFORMATIONS.
Sequence detailsTHE NUMBERING OF RESIDUES IN THE PDB FILE IS BASED ON THE SEQUENCE WITHOUT THE SIGNAL PEPTIDE. THE ...THE NUMBERING OF RESIDUES IN THE PDB FILE IS BASED ON THE SEQUENCE WITHOUT THE SIGNAL PEPTIDE. THE MOLECULE IN THE CRYSTAL IS LACKING THE 14 C-TERMINAL RESIDUES WHICH HAVE BEEN REMOVED BY TREATMENT WITH ENDOPROTEINASE GLUC, MAKING GLU 102, THE NEW C-TERMINUS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 42 %
Crystal growpH: 4.5
Details: 100 MM SODIUM ACETATE, PH 4.5, 5% PEG 8000, 0.5M NACL
Crystal
*PLUS
Density % sol: 43 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 %PEG11
20.5 M11NaCl
30.1 M11NaOAc

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97
DetectorType: ADSC / Detector: CCD / Date: Jan 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 30005 / % possible obs: 83.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.034 / Net I/σ(I): 11.6
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 0.3 / Rsym value: 0.295 / % possible all: 37.3
Reflection
*PLUS
Rmerge(I) obs: 0.034

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
ARPmodel building
DMmodel building
REFMACrefinement
CCP4(SCALA)data scaling
ARP/wARPmodel building
DMphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.5→20 Å / SU ML: 0.063 / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.092
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1500 5 %RANDOM
Rwork0.181 ---
obs-30005 83.9 %-
Displacement parametersBiso mean: 23.6 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1484 0 56 202 1742
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0290.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.6132
X-RAY DIFFRACTIONp_mcangle_it2.6783
X-RAY DIFFRACTIONp_scbond_it2.0072
X-RAY DIFFRACTIONp_scangle_it2.9893
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1410.15
X-RAY DIFFRACTIONp_singtor_nbd0.1710.3
X-RAY DIFFRACTIONp_multtor_nbd0.2560.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.57
X-RAY DIFFRACTIONp_staggered_tor16.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor20.620
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0290.04
X-RAY DIFFRACTIONp_planar_d0.0320.05
X-RAY DIFFRACTIONp_chiral_restr0.1410.15

+
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