[English] 日本語
Yorodumi
- PDB-4lnb: Aspergillus fumigatus protein farnesyltransferase ternary complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lnb
TitleAspergillus fumigatus protein farnesyltransferase ternary complex with farnesyldiphosphate and ethylenediamine scaffold inhibitor 5
Components(CaaX farnesyltransferase ...) x 2
KeywordsTRANSFERASE / isoprenoid and CAAX-containing protein substrate / farnesylation
Function / homology
Function and homology information


peptide pheromone maturation / prenylation / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein geranylgeranyltransferase type I / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / zinc ion binding / cytoplasm
Similarity search - Function
Protein farnesyltransferase subunit beta / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase and squalene oxidase repeat / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid ...Protein farnesyltransferase subunit beta / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase and squalene oxidase repeat / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Chem-ED5 / FARNESYL DIPHOSPHATE / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / Protein farnesyltransferase subunit beta
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.752 Å
AuthorsMabanglo, M.F. / Hast, M.A. / Beese, L.S.
CitationJournal: Protein Sci. / Year: 2014
Title: Crystal structures of the fungal pathogen Aspergillus fumigatus protein farnesyltransferase complexed with substrates and inhibitors reveal features for antifungal drug design.
Authors: Mabanglo, M.F. / Hast, M.A. / Lubock, N.B. / Hellinga, H.W. / Beese, L.S.
History
DepositionJul 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CaaX farnesyltransferase alpha subunit Ram2
B: CaaX farnesyltransferase beta subunit Ram1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,39210
Polymers99,0272
Non-polymers1,3658
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-40 kcal/mol
Surface area29910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.321, 91.253, 83.052
Angle α, β, γ (deg.)90.00, 110.93, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
CaaX farnesyltransferase ... , 2 types, 2 molecules AB

#1: Protein CaaX farnesyltransferase alpha subunit Ram2


Mass: 42391.461 Da / Num. of mol.: 1 / Fragment: unp residues 15-367 / Mutation: N146S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_4G07800, NCBI Locus XM_746952 Ram2 gene / Plasmid: pCDF Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41
References: UniProt: Q4WP27, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Protein CaaX farnesyltransferase beta subunit Ram1


Mass: 56635.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_4G10330, NCBI Locus XM_746700 Ram1 gene / Plasmid: pCDF Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: Q4WPS9, protein farnesyltransferase

-
Non-polymers , 5 types, 541 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE / Farnesyl pyrophosphate


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-ED5 / tert-butyl 4-({(2-{(4-cyanophenyl)[(1-methyl-1H-imidazol-5-yl)methyl]amino}ethyl)[(2-methylphenyl)sulfonyl]amino}methyl)piperidine-1-carboxylate


Mass: 606.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H42N6O4S
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4-10% PEG6000, 600-800 mM LiCl, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 12, 2012
RadiationMonochromator: double crystal liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 88004 / Num. obs: 85716 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.752→37.066 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 18.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1842 3882 4.96 %
Rwork0.1593 --
obs0.1605 83312 94.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.752→37.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6230 0 88 533 6851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036577
X-RAY DIFFRACTIONf_angle_d0.7828952
X-RAY DIFFRACTIONf_dihedral_angle_d12.2112431
X-RAY DIFFRACTIONf_chiral_restr0.059935
X-RAY DIFFRACTIONf_plane_restr0.0031155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7516-1.77160.3333550.32871407X-RAY DIFFRACTION50
1.7716-1.79240.32061010.28061890X-RAY DIFFRACTION67
1.7924-1.81430.27471220.25162088X-RAY DIFFRACTION75
1.8143-1.83720.29221290.24062273X-RAY DIFFRACTION82
1.8372-1.86140.25711390.22382419X-RAY DIFFRACTION87
1.8614-1.88690.25981400.21072526X-RAY DIFFRACTION91
1.8869-1.91380.24531560.20522658X-RAY DIFFRACTION95
1.9138-1.94240.21031280.20022669X-RAY DIFFRACTION96
1.9424-1.97280.22971570.18742708X-RAY DIFFRACTION97
1.9728-2.00510.23231390.18932700X-RAY DIFFRACTION97
2.0051-2.03970.1891610.16832755X-RAY DIFFRACTION98
2.0397-2.07680.20121480.16752723X-RAY DIFFRACTION98
2.0768-2.11670.19851520.16132751X-RAY DIFFRACTION99
2.1167-2.15990.19221430.15992751X-RAY DIFFRACTION99
2.1599-2.20690.17511460.15172778X-RAY DIFFRACTION99
2.2069-2.25820.18141450.15492783X-RAY DIFFRACTION99
2.2582-2.31470.20771560.15162746X-RAY DIFFRACTION99
2.3147-2.37720.19461520.15262774X-RAY DIFFRACTION99
2.3772-2.44720.20271370.14932791X-RAY DIFFRACTION99
2.4472-2.52610.17051360.15112816X-RAY DIFFRACTION99
2.5261-2.61640.16951430.15222758X-RAY DIFFRACTION100
2.6164-2.72110.20571190.15592803X-RAY DIFFRACTION99
2.7211-2.84490.18351390.15552824X-RAY DIFFRACTION100
2.8449-2.99490.18391420.15942815X-RAY DIFFRACTION100
2.9949-3.18240.18291310.15292831X-RAY DIFFRACTION100
3.1824-3.4280.16981560.15282771X-RAY DIFFRACTION100
3.428-3.77260.16551490.14162829X-RAY DIFFRACTION100
3.7726-4.31780.14051440.13692810X-RAY DIFFRACTION100
4.3178-5.43720.15441300.14232842X-RAY DIFFRACTION100
5.4372-37.07440.16771370.1622891X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 25.1534 Å / Origin y: -9.3097 Å / Origin z: 9.4626 Å
111213212223313233
T0.096 Å20.0052 Å2-0.0012 Å2-0.0725 Å20.0086 Å2--0.098 Å2
L0.6844 °20.0084 °2-0.0665 °2-0.5396 °20.1144 °2--0.4927 °2
S-0.0054 Å °-0.0115 Å °0.0087 Å °-0.0244 Å °-0.0073 Å °0.0289 Å °0.0183 Å °-0.016 Å °0.0075 Å °
Refinement TLS groupSelection details: all

+
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