[English] 日本語
Yorodumi
- PDB-9eru: Mouse CNPase catalytic domain with nanobody 7E -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9eru
TitleMouse CNPase catalytic domain with nanobody 7E
Components
  • 2',3'-cyclic-nucleotide 3'-phosphodiesterase
  • Chains: G,C,E,H
KeywordsPROTEIN BINDING / CNPase / myelin / nanobody / single-domain antibody / complex
Function / homology
Function and homology information


cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / myelin sheath adaxonal region / myelin sheath abaxonal region / cyclic nucleotide binding / regulation of mitochondrial membrane permeability / oligodendrocyte differentiation / pseudopodium / microvillus ...cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / myelin sheath adaxonal region / myelin sheath abaxonal region / cyclic nucleotide binding / regulation of mitochondrial membrane permeability / oligodendrocyte differentiation / pseudopodium / microvillus / forebrain development / axonogenesis / adult locomotory behavior / response to toxic substance / melanosome / myelin sheath / response to lipopolysaccharide / mitochondrial outer membrane / mitochondrial inner membrane / perinuclear region of cytoplasm / extracellular space / RNA binding / membrane / cytoplasm
Similarity search - Function
Cyclic nucleotide phosphodiesterase / : / 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase) / Cyclic phosphodiesterase / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMarkusson, S. / Raasakka, A. / Opazo, F. / Kursula, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Mouse CNPase catalytic domain with nanobody 7E
Authors: Markusson, S. / Raasakka, A. / Opazo, F. / Kursula, P.
History
DepositionMar 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
G: Chains: G,C,E,H
A: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
C: Chains: G,C,E,H
D: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
E: Chains: G,C,E,H
F: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
H: Chains: G,C,E,H


Theoretical massNumber of molelcules
Total (without water)152,4218
Polymers152,4218
Non-polymers00
Water543
1
B: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
G: Chains: G,C,E,H


Theoretical massNumber of molelcules
Total (without water)38,1052
Polymers38,1052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-9 kcal/mol
Surface area15800 Å2
MethodPISA
2
A: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
C: Chains: G,C,E,H


Theoretical massNumber of molelcules
Total (without water)38,1052
Polymers38,1052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-10 kcal/mol
Surface area15730 Å2
MethodPISA
3
D: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
E: Chains: G,C,E,H


Theoretical massNumber of molelcules
Total (without water)38,1052
Polymers38,1052
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-9 kcal/mol
Surface area15410 Å2
MethodPISA
4
F: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
H: Chains: G,C,E,H


Theoretical massNumber of molelcules
Total (without water)38,1052
Polymers38,1052
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-8 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.150, 79.000, 117.590
Angle α, β, γ (deg.)77.675, 87.706, 84.290
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein
2',3'-cyclic-nucleotide 3'-phosphodiesterase / CNP / CNPase


Mass: 24236.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Mouse CNPase catalytic domain / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cnp, Cnp1 / Production host: Escherichia coli (E. coli)
References: UniProt: P16330, 2',3'-cyclic-nucleotide 3'-phosphodiesterase
#2: Antibody
Chains: G,C,E,H


Mass: 13868.270 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Anti-CNPase nanobody 7E / Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M MIB pH 4.0, 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 41229 / % possible obs: 91.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 54.93 Å2 / CC1/2: 0.992 / Rrim(I) all: 0.205 / Net I/σ(I): 5.5
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3026 / CC1/2: 0.335 / Rrim(I) all: 2.914 / % possible all: 91.3

-
Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→41.96 Å / SU ML: 0.5228 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 38.4522
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3004 1994 4.85 %
Rwork0.2545 39151 -
obs0.2567 41145 91.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.98 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10333 0 0 3 10336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004110559
X-RAY DIFFRACTIONf_angle_d0.664814271
X-RAY DIFFRACTIONf_chiral_restr0.04351551
X-RAY DIFFRACTIONf_plane_restr0.0041819
X-RAY DIFFRACTIONf_dihedral_angle_d13.52163829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.46391420.45232764X-RAY DIFFRACTION90.87
2.56-2.630.45021380.41382697X-RAY DIFFRACTION87.2
2.63-2.710.39551270.39452513X-RAY DIFFRACTION83.02
2.71-2.80.41481450.3662899X-RAY DIFFRACTION95.1
2.8-2.90.3941490.36262914X-RAY DIFFRACTION94.68
2.9-3.010.41521480.36142903X-RAY DIFFRACTION95.49
3.01-3.150.35291450.32752858X-RAY DIFFRACTION93.79
3.15-3.320.38411470.29292882X-RAY DIFFRACTION93.81
3.32-3.520.29111420.26692776X-RAY DIFFRACTION91.65
3.52-3.790.2941390.24682731X-RAY DIFFRACTION88.33
3.8-4.180.26931380.21612689X-RAY DIFFRACTION87.99
4.18-4.780.21941470.18592897X-RAY DIFFRACTION96.06
4.78-6.020.23271490.20462903X-RAY DIFFRACTION94.28
6.02-41.960.26741380.19922725X-RAY DIFFRACTION89.38

+
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