[English] 日本語
Yorodumi
- PDB-8t70: Cryptococcus neoformans protein farnesyltransferase in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8t70
TitleCryptococcus neoformans protein farnesyltransferase in complex with FPTII and TKCMIIM peptide
Components
  • MET-ILE-ILE-MET
  • Protein farnesyltransferase subunit beta
  • Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
KeywordsTRANSFERASE / Protein prenylyltransferase / TRANSFERASE-substrate complex
Function / homology
Function and homology information


prenylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / zinc ion binding
Similarity search - Function
Protein farnesyltransferase subunit beta / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase alpha-alpha toroid domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid
Similarity search - Domain/homology
Chem-3FX / benzenethiol / Chem-FII / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / Protein farnesyltransferase subunit beta
Similarity search - Component
Biological speciesCryptococcus neoformans (Cryptococcus neoformans serotype A)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 Å
AuthorsWang, Y. / Beese, L.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5P01AI104533 United States
CitationJournal: To Be Published
Title: Cryptococcus neoformans protein farnesyltransferase in complex with FPTII and TKCMIIM peptide
Authors: Wang, Y. / Beese, L.S.
History
DepositionJun 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
B: Protein farnesyltransferase subunit beta
P: MET-ILE-ILE-MET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,23532
Polymers98,5603
Non-polymers2,67429
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14630 Å2
ΔGint36 kcal/mol
Surface area29500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.768, 140.768, 129.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

21B-930-

HOH

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha


Mass: 40913.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (Cryptococcus neoformans serotype A)
Production host: Escherichia coli (E. coli) / References: UniProt: J9VSJ6
#2: Protein Protein farnesyltransferase subunit beta


Mass: 56806.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (Cryptococcus neoformans serotype A)
Production host: Escherichia coli (E. coli) / References: UniProt: T2BPA1

-
Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide MET-ILE-ILE-MET


Mass: 840.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 6 types, 401 molecules

#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-3FX / (2R)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid


Mass: 237.316 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H19NO4S
#7: Chemical ChemComp-FII / [(3,7,11-TRIMETHYL-DODECA-2,6,10-TRIENYLOXYCARBAMOYL)-METHYL]-PHOSPHONIC ACID / FPP ANALOG


Mass: 359.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C17H30NO5P / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-BT6 / benzenethiol


Mass: 110.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6S
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.92 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 100mM CAPSO pH9.5, 50-75mM Li2SO4, 200mM NaCl, 16%-21% PEG4000.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.892→49.77 Å / Num. obs: 103014 / % possible obs: 99.25 % / Redundancy: 5.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.052 / Rrim(I) all: 0.129 / Net I/σ(I): 8.08
Reflection shellResolution: 1.892→1.959 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 1.82 / Num. unique obs: 10141 / CC1/2: 0.931 / Rpim(I) all: 0.306 / Rrim(I) all: 0.755 / % possible all: 98.87

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.892→49.77 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 5171 5.02 %
Rwork0.1849 --
obs0.1861 102952 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.892→49.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6408 0 169 372 6949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.789
X-RAY DIFFRACTIONf_dihedral_angle_d13.2352479
X-RAY DIFFRACTIONf_chiral_restr0.047969
X-RAY DIFFRACTIONf_plane_restr0.0081171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.892-1.910.32673150.28246180X-RAY DIFFRACTION97
1.91-1.940.32873020.27996219X-RAY DIFFRACTION99
1.94-1.960.31093570.26376243X-RAY DIFFRACTION100
1.96-1.980.28253060.2516251X-RAY DIFFRACTION99
1.98-2.010.28323120.24056298X-RAY DIFFRACTION99
2.01-2.040.29373420.23556201X-RAY DIFFRACTION99
2.04-2.070.27723730.23566218X-RAY DIFFRACTION99
2.07-2.10.25032860.22756299X-RAY DIFFRACTION100
2.1-2.130.24633150.20866266X-RAY DIFFRACTION100
2.13-2.170.24033400.20886274X-RAY DIFFRACTION100
2.17-2.20.2553200.21146028X-RAY DIFFRACTION96
2.2-2.240.22423000.20176118X-RAY DIFFRACTION97
2.24-2.290.22633290.20326267X-RAY DIFFRACTION100
2.29-2.330.24813250.19176303X-RAY DIFFRACTION100
2.33-2.380.20393610.18776188X-RAY DIFFRACTION99
2.38-2.440.22763570.18256227X-RAY DIFFRACTION100
2.44-2.50.22782980.18526327X-RAY DIFFRACTION100
2.5-2.570.20413410.18986223X-RAY DIFFRACTION100
2.57-2.640.23783260.19336251X-RAY DIFFRACTION100
2.64-2.730.22733460.18966299X-RAY DIFFRACTION100
2.73-2.830.21453600.19296211X-RAY DIFFRACTION100
2.83-2.940.19663120.19326308X-RAY DIFFRACTION100
2.94-3.070.20573190.19736272X-RAY DIFFRACTION100
3.07-3.230.20793410.19785940X-RAY DIFFRACTION95
3.23-3.440.2243100.19686295X-RAY DIFFRACTION100
3.44-3.70.21143240.18096293X-RAY DIFFRACTION100
3.7-4.070.19533400.1626228X-RAY DIFFRACTION100
4.07-4.660.16573380.14646252X-RAY DIFFRACTION100
4.66-5.870.1963880.15576134X-RAY DIFFRACTION99
5.87-49.770.16362750.15076007X-RAY DIFFRACTION95

+
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