[English] 日本語
Yorodumi
- PDB-1ztg: human alpha polyC binding protein KH1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ztg
Titlehuman alpha polyC binding protein KH1
Components
  • 5'-D(P*CP*CP*CP*TP*CP*CP*CP*T)-3'
  • POLY(RC)-BINDING PROTEIN 1
KeywordsDNA / RNA BINDING PROTEIN/DNA / KH-motif / KH-domain / protein-dna complex / RNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


sequence-specific single stranded DNA binding / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / cytoplasmic ribonucleoprotein granule / single-stranded DNA binding / postsynaptic density / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / ribonucleoprotein complex / cadherin binding ...sequence-specific single stranded DNA binding / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / cytoplasmic ribonucleoprotein granule / single-stranded DNA binding / postsynaptic density / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / ribonucleoprotein complex / cadherin binding / viral RNA genome replication / mRNA binding / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / Poly(rC)-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSidiqi, M. / Wilce, J.A. / Barker, A. / Schmidgerger, J. / Leedman, P.J. / Wilce, M.C.J.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides
Authors: Yoga, Y.M.K. / Traore, D.A.K. / Sidiqi, M. / Szeto, C. / Pendini, N.R. / Barker, A. / Leedman, P.J. / Wilce, J.A. / Wilce, M.C.J.
History
DepositionMay 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2006Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 7, 2012Group: Database references
Revision 1.4Jul 17, 2013Group: Database references
Revision 1.5Oct 25, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: POLY(RC)-BINDING PROTEIN 1
B: POLY(RC)-BINDING PROTEIN 1
C: POLY(RC)-BINDING PROTEIN 1
D: POLY(RC)-BINDING PROTEIN 1
Y: 5'-D(P*CP*CP*CP*TP*CP*CP*CP*T)-3'
Z: 5'-D(P*CP*CP*CP*TP*CP*CP*CP*T)-3'


Theoretical massNumber of molelcules
Total (without water)37,0236
Polymers37,0236
Non-polymers00
Water00
1
A: POLY(RC)-BINDING PROTEIN 1
D: POLY(RC)-BINDING PROTEIN 1
Y: 5'-D(P*CP*CP*CP*TP*CP*CP*CP*T)-3'


Theoretical massNumber of molelcules
Total (without water)18,5113
Polymers18,5113
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: POLY(RC)-BINDING PROTEIN 1
C: POLY(RC)-BINDING PROTEIN 1
Z: 5'-D(P*CP*CP*CP*TP*CP*CP*CP*T)-3'


Theoretical massNumber of molelcules
Total (without water)18,5113
Polymers18,5113
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.6, 76.8, 61.4
Angle α, β, γ (deg.)90.00, 111.7, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12Y
22Z

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEAC13 - 832 - 72
21ILEILEBD13 - 832 - 72
31ILEILECE13 - 832 - 72
41ILEILEDF13 - 832 - 72
12CTYA3 - 101 - 8
22CTZB3 - 101 - 8

NCS ensembles :
ID
1
2

-
Components

#1: Protein
POLY(RC)-BINDING PROTEIN 1 / PCBP1 / ALPHA-CP1 / HNRNP-E1 / NUCLEIC ACID BINDING PROTEIN SUB2.3


Mass: 8106.447 Da / Num. of mol.: 4 / Fragment: KH1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCBP1 / Plasmid: pGEX-6P2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q15365
#2: DNA chain 5'-D(P*CP*CP*CP*TP*CP*CP*CP*T)-3'


Mass: 2298.519 Da / Num. of mol.: 2 / Source method: obtained synthetically

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: cacodylate, MPD, magnesium acetate, NaCl, EDTA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Components of the solutions
IDNameCrystal-IDSol-ID
1cacodylate11
2MPD11
3magnesium acetate11
4NaCl11
5EDTA11
6cacodylate12
7MPD12
8magnesium acetate12
9NaCl12
10EDTA12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Dec 21, 2004 / Details: Osmic
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→45.8 Å / Num. all: 8000 / Num. obs: 7978 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 83 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 22.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EC6 (with oligonucleotide removed)

1ec6


Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 83.054 / SU ML: 0.643 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.516 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29285 368 4.6 %RANDOM
Rwork0.24012 ---
all0.24269 8000 --
obs0.24012 7576 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.058 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 308 0 0 2526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222574
X-RAY DIFFRACTIONr_angle_refined_deg1.3172.1423500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5765285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.97223.95386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.85915467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7061520
X-RAY DIFFRACTIONr_chiral_restr0.0770.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021716
X-RAY DIFFRACTIONr_nbd_refined0.2410.21208
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21759
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.29
X-RAY DIFFRACTIONr_mcbond_it0.1611.51449
X-RAY DIFFRACTIONr_mcangle_it0.2922296
X-RAY DIFFRACTIONr_scbond_it0.44931243
X-RAY DIFFRACTIONr_scangle_it0.6764.51204
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A547medium positional0.530.5
11B547medium positional0.530.5
11C547medium positional0.480.5
11D547medium positional0.550.5
22Y154medium positional0.650.5
11A547medium thermal0.272
11B547medium thermal0.232
11C547medium thermal0.212
11D547medium thermal0.212
22Y154medium thermal0.242
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 29 -
Rwork0.358 577 -
obs--99.67 %
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)
113.32491.1066-1.034315.824-0.851113.89710.22130.47760.5335-1.07250.0764-0.7864-0.90490.0609-0.29770.12870.13710.0175-0.23730.1208-0.0509-1.71820.11424.516
27.94411.903-3.750618.0921-0.196514.21080.58570.53110.64550.9201-0.2060.8478-1.1551-0.5039-0.37970.2141-0.02980.1615-0.3411-0.05140.1349-33.87420.560.511
315.32672.0622-4.077513.85950.339812.6950.320.1282-0.2745-0.0664-0.2167-0.53980.51830.107-0.10330.38110.15410.0226-0.41110.15430.0879-9.2540.807-0.433
410.1811-3.2268-4.673823.21381.18458.6428-0.4505-0.4447-0.58730.4180.0051.01870.43820.08380.44550.2987-0.1682-0.0506-0.2129-0.02170.2599-24.81540.53230.104
517.7750.21820.70720.9496-2.24495.3912-0.56041.3628-0.99480.19090.22440.3255-0.11-0.68170.3360.7359-0.07230.3048-0.0038-0.08650.5847-14.82431.03325.886
629.89252.16717.1763.47950.92176.42460.364-0.7958-0.3951-0.06140.041-0.029-0.2840.1911-0.4050.4861-0.0820.2613-0.17280.2210.3613-20.65630.505-0.198
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC13 - 842 - 73
2X-RAY DIFFRACTION2BD12 - 851 - 74
3X-RAY DIFFRACTION3CE12 - 831 - 72
4X-RAY DIFFRACTION4DF13 - 832 - 72
5X-RAY DIFFRACTION5YA3 - 101 - 8
6X-RAY DIFFRACTION6ZB3 - 101 - 8

+
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