[English] 日本語
Yorodumi
- PDB-3zke: Structure of LC8 in complex with Nek9 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zke
TitleStructure of LC8 in complex with Nek9 peptide
Components
  • DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
  • NEK9 PROTEIN
KeywordsCONTRACTILE PROTEIN/PEPTIDE / CONTRACTILE PROTEIN-PEPTIDE COMPLEX
Function / homology
Function and homology information


nitric-oxide synthase inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / deoxyribonuclease inhibitor activity / intraciliary retrograde transport / Activation of BIM and translocation to mitochondria / motile cilium assembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / ciliary tip / negative regulation of phosphorylation / Intraflagellar transport ...nitric-oxide synthase inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / deoxyribonuclease inhibitor activity / intraciliary retrograde transport / Activation of BIM and translocation to mitochondria / motile cilium assembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / ciliary tip / negative regulation of phosphorylation / Intraflagellar transport / negative regulation of nitric oxide biosynthetic process / Nuclear Pore Complex (NPC) Disassembly / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / cytoplasmic dynein complex / enzyme inhibitor activity / dynein intermediate chain binding / Macroautophagy / protein kinase activator activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / tertiary granule membrane / ficolin-1-rich granule membrane / spermatid development / COPI-mediated anterograde transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / axon cytoplasm / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / substantia nigra development / AURKA Activation by TPX2 / RHO GTPases Activate Formins / cilium / mitotic spindle / kinetochore / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / site of double-strand break / mitotic cell cycle / scaffold protein binding / microtubule / cytoskeleton / non-specific serine/threonine protein kinase / cell division / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA damage response / Neutrophil degranulation / protein-containing complex binding / apoptotic process / protein kinase binding / enzyme binding / mitochondrion / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase Nek9, catalytic domain / : / Regulator of chromosome condensation (RCC1) repeat / Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. ...Serine/threonine-protein kinase Nek9, catalytic domain / : / Regulator of chromosome condensation (RCC1) repeat / Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Dynein light chain 1, cytoplasmic / non-specific serine/threonine protein kinase / Serine/threonine-protein kinase Nek9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGallego, P. / Velazquez-Campoy, A. / Regue, L. / Roig, J. / Reverter, D.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Analysis of the Regulation of the Dynll/Lc8 Binding to Nek9 by Phosphorylation
Authors: Gallego, P. / Velazquez-Campoy, A. / Regue, L. / Roig, J. / Reverter, D.
History
DepositionJan 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2May 15, 2013Group: Database references
Revision 1.3May 22, 2013Group: Derived calculations
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
B: NEK9 PROTEIN
C: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
D: NEK9 PROTEIN
E: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
F: NEK9 PROTEIN
G: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
H: NEK9 PROTEIN
I: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
J: NEK9 PROTEIN
K: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
L: NEK9 PROTEIN


Theoretical massNumber of molelcules
Total (without water)69,00112
Polymers69,00112
Non-polymers00
Water1,928107
1
A: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
B: NEK9 PROTEIN
C: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
D: NEK9 PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,0004
Polymers23,0004
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-23.7 kcal/mol
Surface area8530 Å2
MethodPISA
2
E: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
F: NEK9 PROTEIN
G: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
H: NEK9 PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,0004
Polymers23,0004
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-22.9 kcal/mol
Surface area8420 Å2
MethodPISA
3
I: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
J: NEK9 PROTEIN
K: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
L: NEK9 PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,0004
Polymers23,0004
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-24 kcal/mol
Surface area8550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.984, 105.124, 133.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31D
41F
51I
61K
12G
22C
32E
42H
52J
62L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A5 - 99
2111B940 - 950
3111D940 - 950
4111F941 - 950
5111I5 - 89
6111K5 - 89
1121G5 - 89
2121C5 - 89
3121E5 - 89
4121H940 - 950
5121J940 - 950
6121L940 - 950

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.904569, -0.426259, 0.007678), (-0.426048, 0.903175, -0.05251), (0.015448, -0.050771, -0.998591)-39.42123, -7.97296, 30.43234
3given(0.896908, 0.368707, -0.244154), (0.437957, -0.817068, 0.374959), (-0.061241, -0.443233, -0.894312)29.64951, -29.61178, 18.42435
4given(-0.998837, 0.015332, 0.045704), (0.00907, -0.871377, 0.49053), (0.047347, 0.490374, 0.870225)-53.24747, -48.57833, 13.82059
5given(-0.568661, 0.822378, 0.017871), (0.738398, 0.519923, -0.429473), (-0.362481, -0.231029, -0.902903)25.14783, 50.00758, 2.60422
6given(0.199244, -0.967465, 0.155926), (0.925825, 0.133691, -0.353519), (0.321171, 0.214797, 0.92234)-83.49152, 26.47094, 25.60437

-
Components

#1: Protein
DYNEIN LIGHT CHAIN 1, CYTOPLASMIC / DYNLL-LC8 / 8 KDA DYNEIN LIGHT CHAIN / DLC8 / DYNEIN LIGHT CHAIN LC8-TYPE 1 / PROTEIN INHIBITOR OF ...DYNLL-LC8 / 8 KDA DYNEIN LIGHT CHAIN / DLC8 / DYNEIN LIGHT CHAIN LC8-TYPE 1 / PROTEIN INHIBITOR OF NEURONAL NITRIC OXIDE SYNTHASE / PIN


Mass: 10381.899 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63167
#2: Protein/peptide
NEK9 PROTEIN / NEK9


Mass: 1118.264 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q6PKF2, UniProt: Q8TD19*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.68 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979494
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979494 Å / Relative weight: 1
ReflectionResolution: 2.2→44.63 Å / Num. obs: 28774 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.7 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→82.69 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.483 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.332 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-5 DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.22769 1459 5.1 %RANDOM
Rwork0.19575 ---
obs0.19738 27276 96.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.801 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.89 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 2.2→82.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4619 0 0 107 4726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.024715
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.9246326
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9135563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.32625.135222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.44415869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.589156
X-RAY DIFFRACTIONr_chiral_restr0.1050.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023500
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A6955.57
12B6953.89
13D6954.86
14F6954.53
15I6957.99
16K6958.39
21G694.64
22C693.75
23E695.97
24H694.84
25J693.61
26L699.73
LS refinement shellResolution: 2.197→2.254 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 82 -
Rwork0.265 1710 -
obs--91.01 %

+
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