[English] 日本語
Yorodumi
- PDB-7fiw: Crystal structure of the complex formed by Wolbachia cytoplasmic ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7fiw
TitleCrystal structure of the complex formed by Wolbachia cytoplasmic incompatibility factors CidAwMel(ST) and CidBND1-ND2 from wPip(Pel)
Components
  • ULP_PROTEASE domain-containing protein
  • bacteria factor 4,CidA I(Zeta/1) protein
KeywordsPROTEIN BINDING / Wolbachia / cytoplasmic incompatibility / antitoxin
Function / homologyUlp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / cysteine-type peptidase activity / Papain-like cysteine peptidase superfamily / proteolysis / CidA I(Zeta/1) protein / ULP_PROTEASE domain-containing protein / Cytoplasmic incompatibility factor CifA
Function and homology information
Biological speciesWolbachia endosymbiont of Culex quinquefasciatus Pel (bacteria)
Wolbachia endosymbiont of Drosophila melanogaster (bacteria)
Wolbachia endosymbiont of Culex pipiens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsXiao, Y.J. / Wang, W. / Chen, X. / Ji, X.Y. / Yang, H.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81772204 China
CitationJournal: Nat Commun / Year: 2022
Title: Crystal Structures of Wolbachia CidA and CidB Reveal Determinants of Bacteria-induced Cytoplasmic Incompatibility and Rescue.
Authors: Wang, H. / Xiao, Y. / Chen, X. / Zhang, M. / Sun, G. / Wang, F. / Wang, L. / Zhang, H. / Zhang, X. / Yang, X. / Li, W. / Wei, Y. / Yao, D. / Zhang, B. / Li, J. / Cui, W. / Wang, F. / Chen, C. ...Authors: Wang, H. / Xiao, Y. / Chen, X. / Zhang, M. / Sun, G. / Wang, F. / Wang, L. / Zhang, H. / Zhang, X. / Yang, X. / Li, W. / Wei, Y. / Yao, D. / Zhang, B. / Li, J. / Cui, W. / Wang, F. / Chen, C. / Shen, W. / Su, D. / Bai, F. / Huang, J. / Ye, S. / Zhang, L. / Ji, X. / Wang, W. / Wang, Z. / Hochstrasser, M. / Yang, H.
History
DepositionAug 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ULP_PROTEASE domain-containing protein
B: bacteria factor 4,CidA I(Zeta/1) protein


Theoretical massNumber of molelcules
Total (without water)144,8382
Polymers144,8382
Non-polymers00
Water11,584643
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint8 kcal/mol
Surface area46980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.357, 98.690, 184.847
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ULP_PROTEASE domain-containing protein / bacteria factor 3


Mass: 88873.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolbachia endosymbiont of Culex quinquefasciatus Pel (bacteria)
Strain: wPip / Gene: WP0283 / Production host: Escherichia coli (E. coli) / References: UniProt: B3CP63
#2: Protein bacteria factor 4,CidA I(Zeta/1) protein


Mass: 55964.977 Da / Num. of mol.: 1 / Mutation: R7K,L47Y,P93R,Q288R,Y295S,N299D,G347E,E393R,I397L
Source method: isolated from a genetically manipulated source
Details: Chimeric protein CidASTwMel
Source: (gene. exp.) Wolbachia endosymbiont of Drosophila melanogaster (bacteria), (gene. exp.) Wolbachia endosymbiont of Culex pipiens (bacteria)
Gene: WD_0631 / Production host: Escherichia coli (E. coli) / References: UniProt: Q73HD5, UniProt: A0A5B8WHG9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / 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: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal growTemperature: 289.15 K / Method: batch mode
Details: 5% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.1M HEPES pH 7.5, 10% w/v Polyethylene glycol 10000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 80310 / % possible obs: 98.8 % / Redundancy: 10.8 % / Biso Wilson estimate: 38.53 Å2 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.054 / Rrim(I) all: 0.184 / Χ2: 1.01 / Net I/σ(I): 5.1 / Num. measured all: 868431
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.196.21.04835240.4820.4061.1311.00488
2.19-2.236.90.9737110.5590.3611.041.00993
2.23-2.277.20.84938830.6820.3130.9081.00796.4
2.27-2.328.10.79739830.7570.280.8481.00499.2
2.32-2.379.40.71940150.840.2370.7591.00999.8
2.37-2.42110.68240100.8780.2110.7151.001100
2.42-2.4811.50.63840300.8990.1940.6671.004100
2.48-2.5511.90.56340170.930.1690.5881.008100
2.55-2.6211.80.48940100.9390.1480.5111.003100
2.62-2.7111.60.41140470.9530.1250.431.002100
2.71-2.8110.90.34640410.9660.1090.3641.002100
2.81-2.9211.70.29140470.9750.0880.3041.016100
2.92-3.0512.70.25540510.9830.0740.2651.026100
3.05-3.2112.50.21240300.9870.0620.2210.998100
3.21-3.4112.20.17940960.9890.0530.1871.001100
3.41-3.6811.40.1540760.9910.0460.1571.025100
3.68-4.0512.30.13240800.9930.0390.1381.005100
4.05-4.6312.60.11841390.9950.0340.1231.017100
4.63-5.8311.40.10941720.9940.0330.1141.026100
5.83-5011.70.08743480.9970.0270.0911.01899.7

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FIV

7fiv


Resolution: 2.16→31.62 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2196 2000 2.5 %
Rwork0.192 78142 -
obs0.1926 80142 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.96 Å2 / Biso mean: 49.7114 Å2 / Biso min: 21.85 Å2
Refinement stepCycle: final / Resolution: 2.16→31.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9354 0 0 643 9997
Biso mean---48.43 -
Num. residues----1151
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.16-2.210.32231200.30914694481484
2.21-2.270.31491370.28815347548495
2.27-2.340.33081430.26815553569699
2.34-2.420.30321430.251156195762100
2.42-2.50.26331430.24755845727100
2.5-2.60.26141440.234156305774100
2.6-2.720.27231440.218256375781100
2.72-2.860.23951440.218156385782100
2.86-3.040.2611450.215656665811100
3.04-3.280.21631450.198456625807100
3.28-3.610.20521460.185556905836100
3.61-4.130.19471460.16157205866100
4.13-5.20.17621470.144457835930100
5.2-31.620.17571530.16625919607299
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)
11.31740.5228-0.56882.5892-0.91091.5323-0.0428-0.0964-0.26110.1466-0.0434-0.00790.190.01710.07610.20490.0050.0240.22930.00420.24157.47082.2628113.2833
20.4537-0.5804-0.50111.50861.73542.08070.127-0.03570.24450.0518-0.11770.1345-0.1442-0.1532-0.01880.3109-0.01810.0620.287-0.00850.401349.045634.3544113.0043
32.1666-0.5461-0.08241.93570.15071.57960.1071-0.29410.41320.1537-0.07570.0426-0.20760.0104-0.03130.4148-0.09320.08520.3659-0.08230.384754.480244.0769128.3268
46.63950.3790.35977.04897.30317.5742-0.00420.2491-0.030.2958-0.09850.48710.4953-0.47740.10290.3099-0.0667-0.08370.39180.22340.609444.63945.44989.2307
52.26010.76521.32091.18681.08442.1778-0.215-0.0170.5933-0.19820.18390.8091-0.476-0.59310.02350.42320.0524-0.0380.47310.21320.820845.49558.326490.9196
62.37540.6764-0.15120.3878-0.63772.44710.062-0.22990.34550.1853-0.09820.4226-1.2894-0.4370.03710.68170.08720.08780.37510.07960.937152.331270.6213113.6456
70.4053-0.8904-1.15043.12013.40654.5640.04850.03630.2690.15810.13890.1034-0.10910.0333-0.18510.3560.0073-0.00290.35880.07960.662962.8361.3717101.1845
83.2480.6075-0.6287.69311.83412.3671-0.23120.3410.177-0.20720.4775-0.56390.08740.0912-0.26020.2628-0.0554-0.0540.41020.07620.329368.97541.126182.7323
91.8926-0.28120.14452.3064-0.28771.1966-0.06530.56320.0355-0.30030.0866-0.10480.09710.338-0.02120.2732-0.02170.00110.50490.00210.17457.110619.738279.0351
106.6257-0.04260.31318.1066-0.14093.49240.05080.2007-0.598-0.12880.13540.44110.2147-0.1071-0.17740.2297-0.0349-0.03170.33930.04860.300746.30513.044481.8914
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 337 )A2 - 337
2X-RAY DIFFRACTION2chain 'A' and (resid 338 through 448 )A338 - 448
3X-RAY DIFFRACTION3chain 'A' and (resid 449 through 759 )A449 - 759
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 45 )B4 - 45
5X-RAY DIFFRACTION5chain 'B' and (resid 46 through 106 )B46 - 106
6X-RAY DIFFRACTION6chain 'B' and (resid 107 through 131 )B107 - 131
7X-RAY DIFFRACTION7chain 'B' and (resid 132 through 194 )B132 - 194
8X-RAY DIFFRACTION8chain 'B' and (resid 195 through 286 )B195 - 286
9X-RAY DIFFRACTION9chain 'B' and (resid 287 through 397 )B287 - 397
10X-RAY DIFFRACTION10chain 'B' and (resid 398 through 421 )B398 - 421

+
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