[English] 日本語
Yorodumi
- PDB-2qkd: Crystal structure of tandem ZPR1 domains -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qkd
TitleCrystal structure of tandem ZPR1 domains
ComponentsZinc finger protein ZPR1
KeywordsSIGNALING PROTEIN / CELL CYCLE / HELICAL HAIRPINS / BETA HELIX / ANTI-PARRALLEL BETA SHEET / DOUBLE STRADED ANTI-PARALLEL BETA HELIX / METAL BINDING PROTEIN
Function / homology
Function and homology information


: / pre-mRNA catabolic process / DNA endoreduplication / Cajal body organization / positive regulation of growth / Gemini of coiled bodies / trophectodermal cell proliferation / apoptotic process involved in development / negative regulation of motor neuron apoptotic process / regulation of myelination ...: / pre-mRNA catabolic process / DNA endoreduplication / Cajal body organization / positive regulation of growth / Gemini of coiled bodies / trophectodermal cell proliferation / apoptotic process involved in development / negative regulation of motor neuron apoptotic process / regulation of myelination / inner cell mass cell proliferation / spinal cord development / axon development / Cajal body / translation initiation factor binding / cellular response to epidermal growth factor stimulus / positive regulation of RNA splicing / RNA splicing / receptor tyrosine kinase binding / microtubule cytoskeleton organization / mRNA processing / positive regulation of protein import into nucleus / growth cone / perikaryon / cell population proliferation / axon / neuronal cell body / positive regulation of gene expression / nucleolus / perinuclear region of cytoplasm / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
ZPR1, zinc finger domain / ZPR1, A/B domain / Zinc finger, ZPR1-type / ZPR1 family / ZPR1, A/B domain / ZPR1, zinc finger domain / ZPR1 zinc-finger domain / Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins. / N-terminal domain of TfIIb / Single Sheet ...ZPR1, zinc finger domain / ZPR1, A/B domain / Zinc finger, ZPR1-type / ZPR1 family / ZPR1, A/B domain / ZPR1, zinc finger domain / ZPR1 zinc-finger domain / Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins. / N-terminal domain of TfIIb / Single Sheet / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / Zinc finger protein ZPR1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMishra, A.K.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural insights into the interaction of the evolutionarily conserved ZPR1 domain tandem with eukaryotic EF1A, receptors, and SMN complexes.
Authors: Mishra, A.K. / Gangwani, L. / Davis, R.J. / Lambright, D.G.
History
DepositionJul 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Zinc finger protein ZPR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6324
Polymers45,4551
Non-polymers1773
Water4,954275
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Zinc finger protein ZPR1
hetero molecules

A: Zinc finger protein ZPR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2648
Polymers90,9102
Non-polymers3546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7948.5 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.656, 142.597, 67.219
Angle α, β, γ (deg.)90.00, 114.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-726-

HOH

-
Components

#1: Protein Zinc finger protein ZPR1 / / Zinc finger protein 259


Mass: 45454.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Znf259, Zfp259, Zpr1 / Plasmid: pET15b modified / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q62384
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 14% PEG 6000, 0.2M ammonium sulfate,10% glycerol,2mM tris(2-carboxyethyl)phosphine,0.1M tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.978715 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2004 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978715 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 62931 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 29
Reflection shellResolution: 2→2.04 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 3.16 / Num. unique all: 5305 / Rsym value: 0.348 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: heavy atom model

Resolution: 2→6 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.255 / SU ML: 0.122 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / ESU R: 0.19 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: initial model generated by ARP/wARP was completed by manual building using O and refined in several iterative cycles usingARP/wARP and Refmac5.
RfactorNum. reflection% reflectionSelection details
Rfree0.24736 1569 5.1 %RANDOM
Rwork0.20617 ---
all0.218 ---
obs0.20835 29358 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.135 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å20.73 Å2
2---0.78 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 2 278 3301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223072
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9714154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1685382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27925.395152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11515559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.711520
X-RAY DIFFRACTIONr_chiral_restr0.0820.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022330
X-RAY DIFFRACTIONr_nbd_refined0.2040.21190
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22088
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2252
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.224
X-RAY DIFFRACTIONr_mcbond_it0.8251.51994
X-RAY DIFFRACTIONr_mcangle_it1.38923111
X-RAY DIFFRACTIONr_scbond_it1.97931204
X-RAY DIFFRACTIONr_scangle_it3.1924.51043
LS refinement shellResolution: 2→2.06 Å / Rfactor Rfree error: 0.169 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 108 -
Rwork0.219 2006 -
obs-29358 100 %

+
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