[English] 日本語
Yorodumi
- PDB-9nto: Structure of Cap9-CdnD complex containing NDG modification -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9nto
TitleStructure of Cap9-CdnD complex containing NDG modification
Components
  • Cap9
  • CdnD
KeywordsANTIVIRAL PROTEIN / CD-NTase / QueC / CBASS
Function / homologyChem-2KA / ADENOSINE / ADENOSINE MONOPHOSPHATE
Function and homology information
Biological speciesHyphomicrobiales (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWassarman, D.R. / Pfaff, P. / Paulo, J.A. / Gygi, S.P. / Shokat, K.M. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250-01 United States
Citation
Journal: Science / Year: 2025
Title: Deazaguanylation is a nucleobase-protein conjugation required for type IV CBASS immunity.
Authors: Wassarman, D.R. / Pfaff, P. / Paulo, J.A. / Gygi, S.P. / Shokat, K.M. / Kranzusch, P.J.
#1: Journal: Biorxiv / Year: 2025
Title: Deazaguanylation is a nucleobase-protein conjugation required for type IV CBASS immunity.
Authors: Wassarman, D.R. / Pfaff, P. / Paulo, J.A. / Gygi, S.P. / Shokat, K.M. / Kranzusch, P.J.
History
DepositionMar 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Database references / Category: citation / citation_author
Revision 1.2Oct 8, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CdnD
B: Cap9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3716
Polymers54,4972
Non-polymers8744
Water3,801211
1
A: CdnD
B: Cap9
hetero molecules

A: CdnD
B: Cap9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,74212
Polymers108,9944
Non-polymers1,7488
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area12430 Å2
ΔGint-66 kcal/mol
Surface area37940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.664, 58.219, 89.228
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein CdnD


Mass: 34453.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hyphomicrobiales (bacteria) / Production host: Escherichia coli BW25113 (bacteria)
#2: Protein Cap9


Mass: 20042.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hyphomicrobiales (bacteria) / Production host: Escherichia coli BW25113 (bacteria)

-
Non-polymers , 5 types, 215 molecules

#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-2KA / 2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carboxylic acid


Mass: 194.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6N4O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 24% PEG-3350, 5 mM MgCl2, 1 mM AMP

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 30, 2025
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→43.15 Å / Num. obs: 25975 / % possible obs: 96.43 % / Redundancy: 8.2 % / Biso Wilson estimate: 26.81 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.2997 / Rpim(I) all: 0.1096 / Rrim(I) all: 0.3196 / Net I/σ(I): 6.32
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 8.5 % / Rmerge(I) obs: 2.042 / Num. unique obs: 2661 / CC1/2: 0.378 / CC star: 0.74 / Rpim(I) all: 0.7334 / Rrim(I) all: 2.172 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
AutoProcess1.0.5data processing
Coot0.9.8.95model building
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→43.15 Å / SU ML: 0.2754 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7234
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2317 1359 5.25 %
Rwork0.2048 24529 -
obs0.2063 25888 96.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.7 Å2
Refinement stepCycle: LAST / Resolution: 2.15→43.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 60 211 3743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293597
X-RAY DIFFRACTIONf_angle_d0.56544866
X-RAY DIFFRACTIONf_chiral_restr0.041548
X-RAY DIFFRACTIONf_plane_restr0.0055623
X-RAY DIFFRACTIONf_dihedral_angle_d16.31291314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.230.35861350.31282526X-RAY DIFFRACTION100
2.23-2.320.29121250.29092147X-RAY DIFFRACTION86.26
2.32-2.420.30411180.26452522X-RAY DIFFRACTION99.92
2.42-2.550.30731470.23472487X-RAY DIFFRACTION100
2.55-2.710.25031120.22412295X-RAY DIFFRACTION90.52
2.71-2.920.26821390.21392527X-RAY DIFFRACTION100
2.92-3.220.20751360.19412543X-RAY DIFFRACTION100
3.22-3.680.23221360.18672301X-RAY DIFFRACTION90.53
3.68-4.640.1841610.15722473X-RAY DIFFRACTION96.87
4.64-43.150.19341500.18252708X-RAY DIFFRACTION99.93
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)
12.629556696780.2374009835460.8280944259721.5009561947-0.06316864511491.484161578760.00315906995130.2404699721890.3732814662-0.0277642795596-0.1098822693690.07188369176230.00920070465032-0.09080054888590.1422755967550.2479360137810.0114049143118-0.007902467827660.15931619966-0.0230799400890.132369908309-7.2126165413143.6399576405-17.5513151603
24.060392225241.389395797570.8969796284152.68704600041-0.9509151264740.927613789461-0.412350693175-0.4041364312790.215956018729-0.666620477471-0.193426256267-0.298320172888-0.0123515702815-0.753803793497-0.09488567643610.3249042300380.022209147734-0.003434827668120.550425980233-0.1933343864950.403867916311-29.774895002239.8263245906-26.4726617646
32.0514939177-1.060783444780.1363224964653.16427912796-0.6370130768710.129706565813-0.2213112496370.02028752384610.467935234389-0.5643263932620.03379848355780.943557123811-0.0890883813634-1.19738470237-0.1162755602260.3844995049250.0210760037131-0.1881726835861.13890346543-0.0411651241460.660107464843-39.729928798940.2201218641-32.1584813996
40.2401550311610.3214723809170.5602869971032.35779639902-2.905560931228.25867880257-0.131945965506-0.7428050185740.5442575309510.02030980261070.2362328673050.509267303003-0.0731471602896-1.30573003347-0.06753356031390.6415795489880.357137203338-0.1388719041390.921748317801-0.07870170566130.630644799743-38.615295181847.0037488269-24.8729162342
53.14247426913-0.1020409698060.2564199619722.032747924170.4329015961493.87433209529-0.2029393610820.5535832190960.120815364137-0.2921145386230.01275032313690.490269195366-0.163249911252-0.9270662863030.1408223972250.376584941098-0.0521490655966-0.03937187663030.5439102957440.01093411175090.354511474525-29.734525553735.2490970683-33.1920198436
62.985257082610.4578108038811.104630211282.474703560420.2690660008093.60818981875-0.1284060586150.5874094593770.126660499263-0.3381232699070.0261371304813-0.1262166648890.02475398069850.2402742211860.05412088166850.246334539998-0.00447157777553-0.01621478671540.310793417625-0.02594265592090.194012075202-13.431796315139.7777617052-33.6936013492
71.367109205680.2325134230260.4975226788681.510755527550.6331294700941.8256615787-0.1211388086190.8494582386870.126466533846-0.6102021624430.02948653061120.121217313745-0.124627135372-0.1844531400720.03310579777420.44425747156-0.0237154227606-0.006915621495220.513055111567-0.0278102650190.206292036562-10.943382730743.1237739965-39.494305545
84.218938629830.4998941361842.354219253344.99676319377-2.265111562297.85761905207-0.5602572119630.167111017060.4644094622270.446414954070.248213111430.138492741992-0.240100180027-0.09002762919260.3982087638770.132933526680.01419998401790.0258803450630.121477344773-0.0204466219920.2749523509727.486566827143.4554697437-3.78561649193
91.68509063926-2.544685710930.7897144313166.18615432378-3.929014746395.38238176323-0.073312933867-0.3119649470810.267063884992-0.409666809771-0.0633821488856-0.7200949416350.484812453560.1748079298370.2337821384110.201905038007-0.0474763505882-0.08532095570710.19310955041-0.05731986241310.33282223472514.579556204147.6467879867-6.71292541044
102.62650905038-0.175908554145-0.0482294535975.20686358135-2.683991623094.451758193520.0337968710103-0.427180665179-0.05791911812830.119217252614-0.0007792447840450.902360772344-0.0915543853995-0.3162755167530.07251231627830.131663302692-0.0109264583147-0.09292168368180.154195629933-0.07353272305910.2674346258397.0420966781440.8775375206-0.518204935627
111.638822878160.4884502282320.3301074054272.10895176626-0.8325140978671.802927483860.16317404212-0.05082882077830.2413041717860.0345259264373-0.172486496927-0.125537987051-0.008508762066190.247246532950.08721194462920.327805553046-0.0223450082805-0.09768665337430.191967599639-0.0357154855960.26662498502714.292947858242.84295243336.2385002298
122.491225492220.2430221517160.003491970359490.1621985447490.2917992284312.037403527010.0956281269187-0.485581775566-0.2917673372780.281288674583-0.0181144644022-0.2282800745450.4110269778670.126948089260.01127731008140.29210822849-0.0107020185581-0.03639400996720.215847075670.04047398205050.2574105776578.0953659089829.34660444092.48301239055
131.32289004580.169498758838-0.3724861413831.61758921566-0.2612644816661.4862337280.1066675999310.02566909834460.108315984199-0.0169475056088-0.0764480190932-0.05891206604280.0248696891796-0.0158695295373-0.02859712289470.151715163234-0.0122196606556-0.009840617020690.120964128521-0.01008252582350.2075339466025.6359620201635.6968358625-11.7549665095
140.810853401823-0.9233191074641.399142406593.418406860980.7700437809814.8159948354-0.2707866261780.2869591904380.687238979762-0.311475973509-0.0148830486869-0.290060959412-0.43874174260.560482531269-0.02651790082050.190814485318-0.0558032161796-0.129930991160.1848691879590.05210321066470.53133361794923.736466225746.214965235-5.0959033134
152.01247652066-1.05999578632-0.2375922890123.12934319363-0.2433503797830.2852012236570.41596588763-0.1038173129720.12178505270.2217826671680.180706136927-0.8449165024940.3989822240060.151995066038-0.4385720681050.369972889593-0.011939476733-0.1432461598540.298177879848-0.04807190859930.48653495301423.511266693631.17407101044.29219493727
164.283677222642.38009124952-2.513737551818.264501867991.035438787546.553591003650.3443376818610.2266308229380.4693283006540.563052545126-0.357902346225-0.0876532427879-0.787125931029-0.1118294159050.01134785197460.322272690866-0.0306718956171-0.1461727426780.339317973370.118153561830.67988978556428.464809512634.1963647649-3.26124624346
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 63 )AB3 - 632 - 54
22chain 'A' and (resid 64 through 88 )AB64 - 8855 - 74
33chain 'A' and (resid 89 through 125 )AB89 - 12575 - 106
44chain 'A' and (resid 126 through 143 )AB126 - 143107 - 122
55chain 'A' and (resid 144 through 191 )AB144 - 191123 - 165
66chain 'A' and (resid 192 through 253 )AB192 - 253166 - 227
77chain 'A' and (resid 254 through 309 )AB254 - 309228 - 283
88chain 'B' and (resid 11 through 20 )B000C11 - 201 - 10
99chain 'B' and (resid 21 through 32 )B000C21 - 3211 - 22
1010chain 'B' and (resid 33 through 48 )B000C33 - 4823 - 38
1111chain 'B' and (resid 49 through 63 )B000C49 - 6339 - 53
1212chain 'B' and (resid 64 through 85 )B000C64 - 8554 - 75
1313chain 'B' and (resid 86 through 148 )B000C86 - 14876 - 138
1414chain 'B' and (resid 149 through 165 )B000C149 - 165139 - 155
1515chain 'B' and (resid 166 through 180 )B000C166 - 180156 - 170
1616chain 'B' and (resid 181 through 191 )B000C181 - 191171 - 181

+
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