[English] 日本語
Yorodumi
- PDB-9etj: Mouse CNPase catalytic domain with nanobody 10E -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9etj
TitleMouse CNPase catalytic domain with nanobody 10E
Components
  • 2',3'-cyclic-nucleotide 3'-phosphodiesterase
  • Chains: C,D,F,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: 2.55 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 10E
Authors: Markusson, S. / Raasakka, A. / Opazo, F. / Kursula, P.
History
DepositionMar 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)154,67515
Polymers154,3948
Non-polymers2817
Water00
1
A: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
C: Chains: C,D,F,H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6794
Polymers38,5992
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
D: Chains: C,D,F,H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6794
Polymers38,5992
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
F: Chains: C,D,F,H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6393
Polymers38,5992
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
H: Chains: C,D,F,H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6794
Polymers38,5992
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.730, 118.250, 122.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 162 through 378)
d_2ens_1(chain "B" and (resid 162 through 207 or resid 216 through 290 or resid 297 through 378))
d_3ens_1(chain "E" and (resid 162 through 207 or resid 216 through 291 or resid 298 through 378))
d_4ens_1(chain "G" and (resid 162 through 207 or resid 216 through 291 or resid 298 through 378))
d_1ens_2chain "C"
d_2ens_2chain "D"
d_3ens_2chain "F"
d_4ens_2(chain "H" and resid 2 through 128)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1LYSLYSGLYGLYAA162 - 3784 - 220
d_21ens_1LYSLYSSERSERBC162 - 2074 - 49
d_22ens_1GLUGLUPROPROBC216 - 29058 - 132
d_23ens_1SERSERGLYGLYBC297 - 378139 - 220
d_31ens_1LYSLYSSERSEREE162 - 2074 - 49
d_32ens_1GLUGLUSERSEREE216 - 29158 - 133
d_33ens_1ALAALAGLYGLYEE298 - 378140 - 220
d_41ens_1LYSLYSSERSERGG162 - 2074 - 49
d_42ens_1GLUGLUSERSERGG216 - 29158 - 133
d_43ens_1ALAALAGLYGLYGG298 - 378140 - 220
d_11ens_2VALVALSERSERCB2 - 1282 - 131
d_21ens_2VALVALSERSERDD2 - 1282 - 131
d_31ens_2VALVALSERSERFF2 - 1282 - 131
d_41ens_2VALVALSERSERHH2 - 1282 - 131

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.997718933115, -0.0669895395897, -0.00832658928161), (-0.0672482097991, 0.997082411804, 0.0361156801215), (0.0058829229397, 0.0365932460625, -0.999312926745)17.2582267998, -3.82565677823, 61.5689119675
2given(0.841360488626, -0.404431204684, -0.358535812517), (0.407063957051, 0.910566438565, -0.0718866874289), (0.355543897499, -0.0854643881268, 0.930743990211)42.8021423571, -9.55805135475, -14.2656564156
3given(-0.802158524559, 0.466015114446, 0.373325078966), (0.476240654336, 0.876461668001, -0.0707798253938), (-0.360189589848, 0.12101593958, -0.92499654147)-22.309161563, -6.99960758458, 76.4426651998
4given(-0.997688178001, -0.0586009377953, -0.0344126367374), (-0.0590566794899, 0.998177875369, 0.0123789228693), (0.0336245161353, 0.0143826010613, -0.999331042599)18.1042159177, -3.30722000739, 61.563177991
5given(0.818783344445, -0.455529095725, -0.349409613214), (0.454682191435, 0.886118215291, -0.0897697795602), (0.350510969373, -0.085368328306, 0.932659803396)41.185358455, -9.24940574214, -14.2438138255
6given(-0.777396171421, 0.507643120811, 0.371421128308), (0.51162653962, 0.853815684869, -0.0961096260964), (-0.365914575573, 0.115313651254, -0.923476737778)-20.8033156934, -6.71343813289, 75.9644844074

-
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: C,D,F,H


Mass: 14361.681 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Anti-CNPase nanobody 10E / Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M Na malonate, 20% 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: 2.55→50 Å / Num. obs: 48792 / % possible obs: 99.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 78.4 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.112 / Net I/σ(I): 11.6
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3546 / CC1/2: 0.335 / Rrim(I) all: 3.496 / % possible all: 0.998

-
Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→47.95 Å / SU ML: 0.5623 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.225
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3044 2002 4.12 %
Rwork0.2521 46600 -
obs0.2542 48602 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.03 Å2
Refinement stepCycle: LAST / Resolution: 2.55→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10487 0 7 0 10494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0210744
X-RAY DIFFRACTIONf_angle_d1.61214530
X-RAY DIFFRACTIONf_chiral_restr0.07451529
X-RAY DIFFRACTIONf_plane_restr0.01281872
X-RAY DIFFRACTIONf_dihedral_angle_d14.75823899
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.954295814699
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.31790697938
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.44833835973
ens_2d_2BCX-RAY DIFFRACTIONTorsion NCS0.909642844111
ens_2d_3BCX-RAY DIFFRACTIONTorsion NCS1.23833881777
ens_2d_4BCX-RAY DIFFRACTIONTorsion NCS1.15018776883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.610.46531390.42993250X-RAY DIFFRACTION98.63
2.61-2.680.49351390.42623267X-RAY DIFFRACTION99.39
2.68-2.760.53061440.42683272X-RAY DIFFRACTION99.56
2.76-2.850.51721440.41053291X-RAY DIFFRACTION99.74
2.85-2.950.37931390.36253304X-RAY DIFFRACTION99.74
2.95-3.070.36681390.31843291X-RAY DIFFRACTION99.62
3.07-3.210.35551410.32013309X-RAY DIFFRACTION99.65
3.21-3.380.35031430.32013329X-RAY DIFFRACTION99.91
3.38-3.590.37821410.27733316X-RAY DIFFRACTION99.65
3.59-3.870.32971400.2753322X-RAY DIFFRACTION99.48
3.87-4.260.26851470.23643341X-RAY DIFFRACTION99.63
4.26-4.880.23611420.19183375X-RAY DIFFRACTION99.97
4.88-6.140.27491460.22033403X-RAY DIFFRACTION99.86
6.14-47.950.25331580.2013530X-RAY DIFFRACTION99.41
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)
14.572078418240.4101475317341.733663678642.619091743671.000046121953.416109679-0.156188281634-0.7049144523510.8128677678670.218436463132-0.01092717397240.251142874484-0.648127493068-0.4154993001820.1811881466280.7622997915240.143416987646-0.02407419864030.638954698883-0.06996557513870.636752453194-20.0794836726-6.4538043339822.1940122899
24.78113336822-0.8104166122252.628369083574.01266331828-3.9307351669.487648878130.117389460847-0.0592622846476-0.457380491907-0.0526155500217-0.0326925154092-0.1511390284281.214293720580.648365585571-0.1248226377480.5702689566190.1380889977260.0623989905350.5470266496530.003857467399880.640971901966-7.45925002889-32.049340946925.8460100639
33.181282402790.369131324659-0.352555592333.175623945320.4819530611045.502436878080.04307888194680.6215989955970.594686619996-0.7900031366340.0430211299023-0.188929747316-2.032943831720.379354347814-0.05258331958311.37000305538-0.2250158455950.08079119467920.7637829280430.04445338319930.64227503137437.3189434161-7.9976386216939.004279956
47.678600826852.107866819523.662467027483.201198959941.938144458459.192041917370.09291976340660.347086603641-0.276000613793-0.0480423036511-0.04213065264350.09782949819290.754108427665-0.507536424209-0.09198152724520.4681360762-0.07798739606150.1304111293360.452542623799-0.07447393642690.65156261654626.5373881033-34.538637045535.0237529026
52.32811671123-0.1809106542350.04867047370883.106370420121.695511740566.677787059850.0667635135543-0.02453294363630.2202864590830.0446007888292-0.165235228330.640641319817-0.746209470333-1.060673293980.1466537147680.6828737351160.1953633049310.073020491310.8329998558960.07816134112650.68649701026220.5393983053-25.44201346460.156974669925
63.89548899346-0.222508519797-0.9021799942494.99863071231-2.802654453269.05241667292-0.121786107712-0.202426904011-0.2192854904490.389108663284-0.0921615509645-0.5261639227021.034517120331.271511147160.2919038796710.7011551739480.134671928702-0.02689827910790.570408153121-0.03708984940730.65104432090740.648764409-43.36316083439.98354021541
73.110799566660.344929990434-0.5643137651041.363004588590.1806743025336.503482371730.07097265619010.120518583280.527222618224-0.4435591603810.222986333877-0.550753062596-0.9130545321461.51953280218-0.2581894868670.642652059913-0.2016846945190.06108638033260.907629430094-0.09233486338060.769656989547-0.910969399555-23.968895113462.0017494517
84.79544043571-0.332460196392-0.01709172242575.415041159691.57592794945.986008407050.3566743398750.424846830318-0.122215203503-0.817301012099-0.164630942410.464160878833-0.0715753259764-0.843320568132-0.1434420861950.570431874037-0.00979853061665-0.1198236047740.5413085185410.01055872082620.690377662508-21.7023416411-40.531622796351.2486931452
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 161 through 378)AA161 - 3781 - 204
22(chain 'C' and resid 2 through 128)CB2 - 1281 - 130
33(chain 'B' and resid 162 through 378)BC162 - 3781 - 205
44(chain 'D' and resid 2 through 128)DD2 - 1281 - 130
55(chain 'E' and resid 161 through 378)EE161 - 3781 - 211
66(chain 'F' and resid 2 through 128)FF2 - 1281 - 130
77(chain 'G' and resid 161 through 378)GG161 - 3781 - 211
88(chain 'H' and resid 1 through 128)HH1 - 1281 - 131

+
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