[English] 日本語
Yorodumi
- PDB-1pbw: STRUCTURE OF BCR-HOMOLOGY (BH) DOMAIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pbw
TitleSTRUCTURE OF BCR-HOMOLOGY (BH) DOMAIN
ComponentsPHOSPHATIDYLINOSITOL 3-KINASE
KeywordsPHOSPHOTRANSFERASE / TPASE ACTIVATING PROTEIN / GAP / CDC42 / PHOSPHOINOSITIDE 3-KINASE / SH3 DOMAIN / SH2 DOMAIN / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / phosphatidylinositol kinase activity / positive regulation of focal adhesion disassembly / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulator activity / IRS-mediated signalling / positive regulation of endoplasmic reticulum unfolded protein response / phosphatidylinositol 3-kinase activator activity / interleukin-18-mediated signaling pathway ...perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / phosphatidylinositol kinase activity / positive regulation of focal adhesion disassembly / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulator activity / IRS-mediated signalling / positive regulation of endoplasmic reticulum unfolded protein response / phosphatidylinositol 3-kinase activator activity / interleukin-18-mediated signaling pathway / T follicular helper cell differentiation / phosphatidylinositol 3-kinase complex / PI3K events in ERBB4 signaling / phosphatidylinositol 3-kinase regulatory subunit binding / myeloid leukocyte migration / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / cis-Golgi network / Activated NTRK3 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity / ErbB-3 class receptor binding / Signaling by cytosolic FGFR1 fusion mutants / Co-stimulation by ICOS / RHOD GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / Nephrin family interactions / RHOF GTPase cycle / kinase activator activity / Signaling by LTK in cancer / positive regulation of leukocyte migration / Signaling by LTK / MET activates PI3K/AKT signaling / PI3K/AKT activation / negative regulation of stress fiber assembly / RND1 GTPase cycle / positive regulation of filopodium assembly / RND2 GTPase cycle / RND3 GTPase cycle / growth hormone receptor signaling pathway / insulin binding / Signaling by ALK / PI-3K cascade:FGFR3 / RHOV GTPase cycle / RHOB GTPase cycle / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / natural killer cell mediated cytotoxicity / GP1b-IX-V activation signalling / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / RHOC GTPase cycle / RHOJ GTPase cycle / intracellular glucose homeostasis / negative regulation of osteoclast differentiation / phosphatidylinositol phosphate biosynthetic process / Synthesis of PIPs at the plasma membrane / RHOU GTPase cycle / RET signaling / CDC42 GTPase cycle / PI3K events in ERBB2 signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / insulin receptor substrate binding / T cell differentiation / RHOG GTPase cycle / negative regulation of cell-matrix adhesion / extrinsic apoptotic signaling pathway via death domain receptors / CD28 dependent PI3K/Akt signaling / RHOA GTPase cycle / Role of LAT2/NTAL/LAB on calcium mobilization / RAC2 GTPase cycle / RAC3 GTPase cycle / Interleukin receptor SHC signaling / Role of phospholipids in phagocytosis / GAB1 signalosome / enzyme-substrate adaptor activity / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / phosphatidylinositol 3-kinase binding / Signaling by FGFR4 in disease / GPVI-mediated activation cascade / positive regulation of lamellipodium assembly / Signaling by FLT3 ITD and TKD mutants / Signaling by FGFR3 in disease / Tie2 Signaling / insulin-like growth factor receptor binding / Signaling by FGFR2 in disease / phosphotyrosine residue binding / RAC1 GTPase cycle / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / positive regulation of smooth muscle cell proliferation / Downstream signal transduction / substrate adhesion-dependent cell spreading / Interleukin-7 signaling / insulin-like growth factor receptor signaling pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / osteoclast differentiation / response to endoplasmic reticulum stress
Similarity search - Function
Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / Rho GTPase-activating protein domain / RhoGAP domain ...Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphatidylinositol 3-kinase regulatory subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsMusacchio, A. / Cantley, L.C. / Harrison, S.C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Crystal structure of the breakpoint cluster region-homology domain from phosphoinositide 3-kinase p85 alpha subunit.
Authors: Musacchio, A. / Cantley, L.C. / Harrison, S.C.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1991
Title: Cloning of Pi3 Kinase-Associated P85 Utilizing a Novel Method for Expression/Cloning of Target Proteins for Receptor Tyrosine Kinases
Authors: Skolnik, E.Y. / Margolis, B. / Mohammadi, M. / Lowenstein, E. / Fischer, R. / Drepps, A. / Ullrich, A. / Schlessinger, J.
History
DepositionOct 17, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHATIDYLINOSITOL 3-KINASE
B: PHOSPHATIDYLINOSITOL 3-KINASE


Theoretical massNumber of molelcules
Total (without water)48,6082
Polymers48,6082
Non-polymers00
Water4,810267
1
A: PHOSPHATIDYLINOSITOL 3-KINASE


Theoretical massNumber of molelcules
Total (without water)24,3041
Polymers24,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHOSPHATIDYLINOSITOL 3-KINASE


Theoretical massNumber of molelcules
Total (without water)24,3041
Polymers24,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.051, 90.513, 69.280
Angle α, β, γ (deg.)90.00, 97.19, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.055, 0.719, 0.413), (0.674, 0.102, 0.731), (0.483, 0.687, -0.542)
Vector: 6.259, -6.386, 3.622)

-
Components

#1: Protein PHOSPHATIDYLINOSITOL 3-KINASE / RHOGAP DOMAIN


Mass: 24304.002 Da / Num. of mol.: 2 / Fragment: P85 ALPHA SUBUNIT BCR-HOMOLOGY DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: T7-BASED EXPRESSION SYSTEM / Plasmid: PBAT4 / Production host: Escherichia coli (E. coli) / References: UniProt: P27986
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 40 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
23.6 Msodium formate1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 6, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 30040 / % possible obs: 95 % / Redundancy: 2.54 % / Rmerge(I) obs: 0.057
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 124328
Reflection shell
*PLUS
% possible obs: 84 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 5.4

-
Processing

Software
NameVersionClassification
ARP/wARPmodel building
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 2→8 Å / σ(F): 0
RfactorNum. reflection
Rfree0.235 -
Rwork0.184 -
obs0.184 29354
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5469 0 0 267 5736
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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