[English] 日本語
Yorodumi
- PDB-2yab: Crystal structure of the autoinhibited form of mouse DAPK2 in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yab
TitleCrystal structure of the autoinhibited form of mouse DAPK2 in complex with AMP
ComponentsDEATH-ASSOCIATED PROTEIN KINASE 2
KeywordsTRANSFERASE / APOPTOSIS
Function / homology
Function and homology information


autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / neutrophil migration / cytoplasmic vesicle / non-specific serine/threonine protein kinase / calmodulin binding / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity ...autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / neutrophil migration / cytoplasmic vesicle / non-specific serine/threonine protein kinase / calmodulin binding / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / ATP binding / nucleus / cytoplasm
Similarity search - Function
Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Death-associated protein kinase 2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPatel, A.K. / Kursula, P.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structure of the Dimeric Autoinhibited Conformation of Dapk2, a Pro-Apoptotic Protein Kinase.
Authors: Patel, A.K. / Yadav, R.P. / Majava, V. / Kursula, I. / Kursula, P.
History
DepositionFeb 18, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DEATH-ASSOCIATED PROTEIN KINASE 2
B: DEATH-ASSOCIATED PROTEIN KINASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,80710
Polymers83,5922
Non-polymers1,2158
Water12,358686
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-66.2 kcal/mol
Surface area26740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.140, 85.370, 123.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DEATH-ASSOCIATED PROTEIN KINASE 2 / DAP-KINASE-RELATED PROTEIN 1 / DAP KINASE 2 / DRP-1


Mass: 41795.848 Da / Num. of mol.: 2 / Fragment: RESIDUES 13-311
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PTH27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS RARE
References: UniProt: Q8VDF3, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / 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 Å3/Da / Density % sol: 38.46 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 53144 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 20.31 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.2
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.3 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A2A

2a2a


Resolution: 1.9→42.685 Å / SU ML: 0.22 / σ(F): 1.99 / Phase error: 21.76 / Stereochemistry target values: ML
Details: THE C-TERMINAL 59 RESIDUES ARE NOT VISIBLE IN ELECTRON DENSITY, MOST LIKELY THE C-TERMINAL TAIL HAS DEGRADED DURING CRYSTALLIZATION.
RfactorNum. reflection% reflection
Rfree0.2148 2658 5 %
Rwork0.1718 --
obs0.1739 53125 99.24 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.327 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 30.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.1984 Å20 Å20 Å2
2--4.0243 Å20 Å2
3----5.2227 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4852 0 72 686 5610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065174
X-RAY DIFFRACTIONf_angle_d1.0237017
X-RAY DIFFRACTIONf_dihedral_angle_d15.6181967
X-RAY DIFFRACTIONf_chiral_restr0.061783
X-RAY DIFFRACTIONf_plane_restr0.004902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9003-1.93480.3041350.252552X-RAY DIFFRACTION97
1.9348-1.9720.26991380.21832623X-RAY DIFFRACTION99
1.972-2.01230.25451370.20042612X-RAY DIFFRACTION99
2.0123-2.0560.23781380.18472625X-RAY DIFFRACTION99
2.056-2.10390.22261390.17662629X-RAY DIFFRACTION100
2.1039-2.15650.21621390.17352638X-RAY DIFFRACTION100
2.1565-2.21480.23671390.15732641X-RAY DIFFRACTION99
2.2148-2.27990.2331370.17142617X-RAY DIFFRACTION99
2.2799-2.35350.2261390.16062633X-RAY DIFFRACTION100
2.3535-2.43760.25181400.16932664X-RAY DIFFRACTION100
2.4376-2.53520.21851400.17072653X-RAY DIFFRACTION99
2.5352-2.65060.23471390.17062644X-RAY DIFFRACTION99
2.6506-2.79030.26661390.1632637X-RAY DIFFRACTION99
2.7903-2.96510.20911410.16432687X-RAY DIFFRACTION99
2.9651-3.1940.2411400.17562659X-RAY DIFFRACTION99
3.194-3.51520.2251420.17842696X-RAY DIFFRACTION100
3.5152-4.02360.17521420.14542697X-RAY DIFFRACTION100
4.0236-5.0680.14381440.1442730X-RAY DIFFRACTION99
5.068-42.69580.20231500.20072830X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.11250.2165-0.08430.6673-0.27630.2098-0.28830.0986-0.1369-0.40960.04010.08870.2959-0.0582-0.02320.23310.1234-0.00310.1364-0.02170.1871-13.5106-15.6216-32.0117
20.54810.0216-0.39490.15570.4041.5080.36330.15290.0776-0.5480.19880.1961-0.05560.18830.08110.31650.0695-0.08610.15390.04640.2254-15.0793-1.4935-41.2925
30.5818-0.46160.06350.5251-0.11350.36050.0325-0.0188-0.0752-0.0469-0.00590.05050.06230.0302-0.01460.0979-0.0032-0.01560.0938-0.00390.1052-20.5794-1.1363-22.3977
40.6357-0.0883-0.09030.1669-0.12910.59710.0153-0.04170.0011-0.03790.02430.0337-0.0743-0.1038-0.0160.0919-0.00310.00090.09070.00490.0844-34.208110.873-20.4146
50.5969-0.0684-0.0050.3329-0.2610.51850.048-0.0385-0.12120.0908-0.0368-0.02-0.0837-0.05130.00590.1619-0.0291-0.03090.15890.0130.1574-49.4965-16.4862-50.8181
60.93720.0006-0.07770.2584-0.01940.82010.1062-0.08570.13940.28230.0074-0.0322-0.0883-0.2193-0.00350.2307-0.0244-0.03860.1595-0.02790.1577-47.6242-1.845-41.3291
70.54190.49620.23680.6480.27020.17050.00850.1214-0.11340.06980.0395-0.16160.0212-0.0112-0.01580.11570.035-0.01240.12130.00640.1398-42.593-3.6169-61.476
80.46680.0971-0.01010.24340.0050.5330.17950.0558-0.0662-0.0849-0.0706-0.0226-0.12550.036-0.02860.11930.0183-0.01720.1362-0.01960.1141-40.2548-2.4687-60.873
90.8050.0042-0.30810.42860.29310.98140.05980.05750.1047-0.0385-0.0179-0.0411-0.12040.0959-0.03380.13020.01150.02680.12240.00970.1048-31.567512.5005-58.6982
100.04130.05970.01030.14870.05340.03240.02160.4738-0.0658-0.05390.03840.0499-0.1804-0.1520.11690.01930.09290.21290.3358-0.06260.2406-24.87892.7339-73.6507
110.0555-0.01920.02510.06230.00180.1517-0.0404-0.10410.0074-0.03630.01720.04080.0087-0.0189-0.03750.15290.0394-0.12160.2195-0.14970.196-22.4401-8.3704-28.6738
120.07310.03550.06170.05460.04820.0893-0.06850.0374-0.06360.0323-0.0328-0.0518-0.0067-0.046-0.00430.13880.0163-0.06410.20070.04820.16-40.0624-9.625-54.8436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 3:45)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 46:70)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 71:174)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 175:301)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 3:45)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 46:70)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 71:133)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 134:164)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 165:279)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 280:301)
11X-RAY DIFFRACTION11CHAIN A AND (RESSEQ 1302:1302)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 1302:1302)

+
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://pdbjlvh1.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