[English] 日本語
Yorodumi
- PDB-4y94: Crystal structure of the PH-TH module of Bruton's tyrosine kinase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y94
TitleCrystal structure of the PH-TH module of Bruton's tyrosine kinase bound to inositol hexakisphosphate
ComponentsNon-specific protein-tyrosine kinase
KeywordsTRANSFERASE / Btk / PH domain / tyrosine kinase / inositol hexakisphosphate
Function / homology
Function and homology information


FCERI mediated Ca+2 mobilization / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / DAP12 signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / B cell affinity maturation / positive regulation of cGAS/STING signaling pathway / cellular response to interleukin-7 / G alpha (12/13) signalling events / G beta:gamma signalling through BTK ...FCERI mediated Ca+2 mobilization / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / DAP12 signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / B cell affinity maturation / positive regulation of cGAS/STING signaling pathway / cellular response to interleukin-7 / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / negative regulation of cytokine production / G alpha (q) signalling events / phospholipase activator activity / negative regulation of B cell proliferation / positive regulation of NLRP3 inflammasome complex assembly / phospholipase binding / phosphatidylinositol-3,4,5-trisphosphate binding / cell maturation / non-membrane spanning protein tyrosine kinase activity / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / T cell receptor signaling pathway / cytoplasmic vesicle / adaptive immune response / intracellular signal transduction / membrane raft / zinc ion binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Tyrosine-protein kinase BTK, SH3 domain / Zinc finger, Btk motif / BTK motif / Zinc finger Btk-type profile. / Bruton's tyrosine kinase Cys-rich motif / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / : / PH domain profile. ...Tyrosine-protein kinase BTK, SH3 domain / Zinc finger, Btk motif / BTK motif / Zinc finger Btk-type profile. / Bruton's tyrosine kinase Cys-rich motif / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / : / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / PH-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Tyrosine-protein kinase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsWang, Q. / Kuriyan, J.
CitationJournal: Elife / Year: 2015
Title: Autoinhibition of Bruton's tyrosine kinase (Btk) and activation by soluble inositol hexakisphosphate.
Authors: Wang, Q. / Vogan, E.M. / Nocka, L.M. / Rosen, C.E. / Zorn, J.A. / Harrison, S.C. / Kuriyan, J.
History
DepositionFeb 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / entity_src_gen / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Feb 28, 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
B: Non-specific protein-tyrosine kinase
C: Non-specific protein-tyrosine kinase
A: Non-specific protein-tyrosine kinase
D: Non-specific protein-tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,86714
Polymers80,6454
Non-polymers4,22210
Water77543
1
A: Non-specific protein-tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5474
Polymers20,1611
Non-polymers1,3853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-specific protein-tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8873
Polymers20,1611
Non-polymers7252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Non-specific protein-tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8873
Polymers20,1611
Non-polymers7252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Non-specific protein-tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5474
Polymers20,1611
Non-polymers1,3853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.203, 64.012, 80.029
Angle α, β, γ (deg.)82.080, 88.790, 89.890
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA2 - 999
211chain BB0 - 999
311chain CC2 - 999
411chain DD0 - 999

-
Components

#1: Protein
Non-specific protein-tyrosine kinase


Mass: 20161.178 Da / Num. of mol.: 4 / Fragment: PH domain (UNP residues 1-170)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: BTK / Production host: Escherichia coli (E. coli)
References: UniProt: Q3ZC95, non-specific protein-tyrosine kinase
#2: Chemical
ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 1500, 0.1 M DL-malic acid, 3 mM potasium myo-inositol hexakisphosphate
PH range: 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. obs: 30522 / % possible obs: 94.9 % / Redundancy: 2 % / Biso Wilson estimate: 52.82 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.055 / Rrim(I) all: 0.082 / Χ2: 0.987 / Net I/av σ(I): 10.82 / Net I/σ(I): 12.4 / Num. measured all: 61653
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.31-2.391.70.53823140.5540.5190.7480.78771.8
2.39-2.491.90.47829730.6590.4570.6630.7992.7
2.49-2.620.34730630.7750.3260.4770.84896.7
2.6-2.742.10.25631800.860.2390.3510.94897.5
2.74-2.912.10.18331410.9280.1710.2511.09397.7
2.91-3.132.10.12131510.9690.1120.1660.9498.1
3.13-3.452.10.0831460.9830.0740.1091.05498.4
3.45-3.952.10.05731820.9890.0510.0771.20198.7
3.95-4.982.10.04231930.9930.0380.0571.01398.8
4.98-5020.04231790.9950.0370.0561.02498.9

-
Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
RefinementResolution: 2.4→46.483 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2553 1855 6.64 %
Rwork0.2294 26072 -
obs0.2311 27927 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.62 Å2 / Biso mean: 56.9964 Å2 / Biso min: 24.57 Å2
Refinement stepCycle: final / Resolution: 2.4→46.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5130 0 220 43 5393
Biso mean--87.67 58.12 -
Num. residues----617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065466
X-RAY DIFFRACTIONf_angle_d1.1677442
X-RAY DIFFRACTIONf_chiral_restr0.064796
X-RAY DIFFRACTIONf_plane_restr0.009900
X-RAY DIFFRACTIONf_dihedral_angle_d15.982131
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3082X-RAY DIFFRACTION10.092TORSIONAL
12B3082X-RAY DIFFRACTION10.092TORSIONAL
13C3082X-RAY DIFFRACTION10.092TORSIONAL
14D3082X-RAY DIFFRACTION10.092TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.46490.36691400.31881948208893
2.4649-2.53740.34311360.30111925206196
2.5374-2.61930.32751460.28652010215697
2.6193-2.71290.34931390.25572001214098
2.7129-2.82150.28051480.26281999214798
2.8215-2.94990.34481410.24932007214898
2.9499-3.10540.27731450.24282029217498
3.1054-3.29990.281390.2442011215098
3.2999-3.55470.24961460.22592021216799
3.5547-3.91220.26661420.22052029217199
3.9122-4.47790.20961390.20622032217199
4.4779-5.64010.21761420.21122033217599
5.6401-46.49220.23791520.222027217999

+
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