[English] 日本語
Yorodumi
- PDB-3iij: The structure of hCINAP-ADP complex at 1.76 angstroms resolution. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3iij
TitleThe structure of hCINAP-ADP complex at 1.76 angstroms resolution.
ComponentsCoilin-interacting nuclear ATPase protein
KeywordsPROTEIN BINDING / TRANSFERASE / Alpha and beta proteins (a/b) / phosphotransferase
Function / homology
Function and homology information


nucleoside monophosphate kinase activity / adenylate kinase / adenylate kinase activity / nucleobase-containing small molecule interconversion / Interconversion of nucleotide di- and triphosphates / Cajal body / nuclear speck / phosphorylation / centrosome / ATP hydrolysis activity ...nucleoside monophosphate kinase activity / adenylate kinase / adenylate kinase activity / nucleobase-containing small molecule interconversion / Interconversion of nucleotide di- and triphosphates / Cajal body / nuclear speck / phosphorylation / centrosome / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
Adenylate kinase isoenzyme 6 / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Adenylate kinase isoenzyme 6 / Adenylate kinase isoenzyme 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsZographos, S.E. / Drakou, C.E. / Leonidas, D.D.
CitationJournal: Proteins / Year: 2012
Title: hCINAP is an atypical mammalian nuclear adenylate kinase with an ATPase motif: Structural and functional studies.
Authors: Drakou, C.E. / Malekkou, A. / Hayes, J.M. / Lederer, C.W. / Leonidas, D.D. / Oikonomakos, N.G. / Lamond, A.I. / Santama, N. / Zographos, S.E.
History
DepositionAug 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Advisory / Database references
Revision 1.3Nov 23, 2011Group: Database references
Revision 1.4Jan 18, 2012Group: Database references
Revision 1.5Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Coilin-interacting nuclear ATPase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6796
Polymers20,8671
Non-polymers8115
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.144, 99.144, 57.838
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Coilin-interacting nuclear ATPase protein / Coilin-interacting nuclear ATPase protein / TAF9 RNA polymerase II / TATA box binding protein (TBP)- ...Coilin-interacting nuclear ATPase protein / TAF9 RNA polymerase II / TATA box binding protein (TBP)-associated factor / 32kDa / isoform CRA_b / human adenylate kinase 6


Mass: 20867.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CINAP, TAF9, hCG_37060 / Plasmid: pGEX-6P-3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5F2S9, UniProt: Q9Y3D8*PLUS, adenylate kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.93 Å3/Da / Density % sol: 68.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1.5 M Li2SO4, 0.2 M NaCl, 0.5 mM DTT, 25 mM MgCl2, 2 mM ADP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.11665 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2007 / Details: Rh Coated mirrors
RadiationMonochromator: double crystal monochromator with sagittal focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11665 Å / Relative weight: 1
ReflectionResolution: 1.76→30 Å / Num. all: 32104 / Num. obs: 31610 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 32.8 Å2 / Rsym value: 0.044 / Net I/σ(I): 17.92
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.41 / Rsym value: 0.499 / % possible all: 88.4

-
Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RKB

1rkb


Resolution: 1.76→28.3 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.051 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.089 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19509 1595 5 %RANDOM
Rwork0.18121 ---
all0.18193 31610 --
obs0.18193 30007 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.76→28.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 47 190 1678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221547
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.9952110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6855180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31525.81486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86215269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.765157
X-RAY DIFFRACTIONr_chiral_restr0.0770.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211182
X-RAY DIFFRACTIONr_mcbond_it0.4541.5883
X-RAY DIFFRACTIONr_mcangle_it0.87621441
X-RAY DIFFRACTIONr_scbond_it1.4483664
X-RAY DIFFRACTIONr_scangle_it2.3934.5667
LS refinement shellResolution: 1.76→1.809 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 108 -
Rwork0.271 2220 -
obs--98.85 %
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)
113.813-1.381110.01457.57433.0159.4309-0.0246-0.3691-0.1618-0.9832-0.72161.6303-0.5592-0.6840.74620.17530.0673-0.16760.4348-0.0380.478712.161-56.55928.9306
22.08820.4062-0.91951.0309-0.39481.2113-0.00220.1463-0.12860.0023-0.04490.06770.0144-0.0170.04710.0981-0.0135-0.01020.1392-0.00370.127933.1153-54.1185-1.0799
31.84651.8132-0.78366.1885-1.61981.65470.030.3066-0.1988-0.0204-0.04880.14150.1185-0.17090.01880.067-0.0348-0.03310.1545-0.02580.131125.713-55.9728-4.0961
42.7023.1579-0.84729.91891.13118.5388-0.04290.2577-0.1053-0.4883-0.013-0.34020.027-0.0430.05590.08470.0131-0.03710.19250.07940.107126.5114-39.6215-11.2955
54.8596-1.88138.02023.7805-3.44813.28170.37541.488-0.4913-0.34680.1399-1.40370.53212.4197-0.51540.0660.09870.15740.83-0.18881.256240.022-35.726-13.1507
66.98942.7045-2.98987.2455-4.94367.1413-0.01820.24370.35670.18950.02840.5149-0.4373-0.2661-0.01020.10120.053-0.01690.11080.02540.133323.2585-40.28740.5805
71.9766-0.1372-0.11290.8787-0.33850.88480.01970.06460.06930.1204-0.01620.0386-0.1504-0.0186-0.00350.1213-0.0155-0.00340.11990.00640.104832.0963-48.14443.4831
88.9923-0.8466-0.11031.8333-1.47133.8236-0.05320.8481-0.2959-0.2304-0.0603-0.14810.0847-0.04990.11350.0827-0.00190.01590.1871-0.04550.104346.899-56.5523-11.643
95.82960.40074.22533.35284.15539.7578-0.09550.9230.3432-0.47270.1264-0.0047-0.50350.0442-0.03080.0872-0.05980.02260.37430.13860.156247.9449-46.464-14.05
107.0244-1.8726-4.47682.55373.24115.8630.1117-0.22340.20220.0483-0.0123-0.3177-0.03030.1291-0.09940.0795-0.0159-0.02050.1450.03720.153647.8213-47.96670.6375
112.8105-0.0313-0.68354.61031.71263.3257-0.1415-0.2008-0.34870.21240.0412-0.1280.150.27360.10030.08460.0065-0.01330.12440.03750.129339.0907-57.864.6243
125.0648-1.1311-2.26113.59972.26273.88210.0242-0.2814-0.19040.28710.0049-0.14620.12870.0841-0.02910.142-0.0464-0.00690.10430.02520.13525.8998-62.105310.8767
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 2
2X-RAY DIFFRACTION2A3 - 20
3X-RAY DIFFRACTION3A21 - 36
4X-RAY DIFFRACTION4A37 - 45
5X-RAY DIFFRACTION5A46 - 56
6X-RAY DIFFRACTION6A57 - 71
7X-RAY DIFFRACTION7A72 - 96
8X-RAY DIFFRACTION8A97 - 109
9X-RAY DIFFRACTION9A110 - 120
10X-RAY DIFFRACTION10A121 - 131
11X-RAY DIFFRACTION11A132 - 155
12X-RAY DIFFRACTION12A156 - 172

+
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