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- PDB-6o60: Crystal structure of GGTase3-FBXL2-SKP1 complex -

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Basic information

Entry
Database: PDB / ID: 6o60
TitleCrystal structure of GGTase3-FBXL2-SKP1 complex
Components
  • F-box/LRR-repeat protein 2
  • Geranylgeranyl transferase type-2 subunit beta
  • Protein prenyltransferase alpha subunit repeat-containing protein 1
  • S-phase kinase-associated protein 1
KeywordsTRANSFERASE / F-box / Leucine-rich repeat / GGTase subunits
Function / homology
Function and homology information


protein prenyltransferase activity / protein geranylgeranyltransferase type II / Rab-protein geranylgeranyltransferase complex / host-mediated perturbation of viral RNA genome replication / Rab geranylgeranyltransferase activity / protein geranylgeranylation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / F-box domain binding / PcG protein complex / negative regulation of NLRP3 inflammasome complex assembly ...protein prenyltransferase activity / protein geranylgeranyltransferase type II / Rab-protein geranylgeranyltransferase complex / host-mediated perturbation of viral RNA genome replication / Rab geranylgeranyltransferase activity / protein geranylgeranylation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / F-box domain binding / PcG protein complex / negative regulation of NLRP3 inflammasome complex assembly / phosphatidylinositol 3-kinase regulatory subunit binding / RAB geranylgeranylation / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / ubiquitin ligase complex scaffold activity / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / cullin family protein binding / protein monoubiquitination / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / visual perception / molecular function activator activity / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / beta-catenin binding / Degradation of beta-catenin by the destruction complex / protein modification process / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / small GTPase binding / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Interleukin-1 signaling / protein polyubiquitination / Orc1 removal from chromatin / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / : / Regulation of PLK1 Activity at G2/M Transition / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / regulation of inflammatory response / protein phosphatase binding / proteasome-mediated ubiquitin-dependent protein catabolic process / calmodulin binding / regulation of autophagy / protein ubiquitination / chromatin remodeling / protein domain specific binding / centrosome / mitochondrion / proteolysis / zinc ion binding / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Geranylgeranyl transferase type-2 subunit beta / F-box domain / Prenyltransferase subunit beta / A Receptor for Ubiquitination Targets / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Leucine-rich repeat, cysteine-containing subtype ...: / Geranylgeranyl transferase type-2 subunit beta / F-box domain / Prenyltransferase subunit beta / A Receptor for Ubiquitination Targets / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box domain profile. / Prenyltransferase alpha-alpha toroid domain / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Glycosyltransferase - #20 / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Leucine Rich repeat / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Geranylgeranyl transferase type-2 subunit beta / S-phase kinase-associated protein 1 / Protein prenyltransferase alpha subunit repeat-containing protein 1 / F-box/LRR-repeat protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsWang, H. / Zheng, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: GGTase3 is a newly identified geranylgeranyltransferase targeting a ubiquitin ligase.
Authors: Kuchay, S. / Wang, H. / Marzio, A. / Jain, K. / Homer, H. / Fehrenbacher, N. / Philips, M.R. / Zheng, N. / Pagano, M.
History
DepositionMar 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: 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
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein prenyltransferase alpha subunit repeat-containing protein 1
B: Geranylgeranyl transferase type-2 subunit beta
C: F-box/LRR-repeat protein 2
D: S-phase kinase-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,9025
Polymers149,8364
Non-polymers651
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10310 Å2
ΔGint-70 kcal/mol
Surface area47790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.843, 99.318, 151.202
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Protein prenyltransferase alpha subunit repeat-containing protein 1


Mass: 46813.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTAR1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7Z6K3
#2: Protein Geranylgeranyl transferase type-2 subunit beta / Geranylgeranyl transferase type II subunit beta / GGTase-II-beta / Rab geranyl-geranyltransferase ...Geranylgeranyl transferase type II subunit beta / GGTase-II-beta / Rab geranyl-geranyltransferase subunit beta / Rab GGTase beta / Rab geranylgeranyltransferase subunit beta / Type II protein geranyl-geranyltransferase subunit beta


Mass: 37047.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RABGGTB, GGTB / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P53611, protein geranylgeranyltransferase type II
#3: Protein F-box/LRR-repeat protein 2 / F-box and leucine-rich repeat protein 2 / F-box protein FBL2/FBL3


Mass: 47208.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBXL2, FBL2, FBL3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UKC9
#4: Protein S-phase kinase-associated protein 1 / Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti ...Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti protein II / OCP-II / RNA polymerase II elongation factor-like protein / SIII / Transcription elongation factor B polypeptide 1-like / p19skp1


Mass: 18767.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P63208

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Non-polymers , 2 types, 71 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH6.0, 20%-22% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 41359 / % possible obs: 90.5 % / Redundancy: 4.8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.098 / Net I/σ(I): 24.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2100 / CC1/2: 0.754 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DSS and 1FQV

3dss

1fqv


Resolution: 2.503→49.451 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.51
RfactorNum. reflection% reflection
Rfree0.247 2069 5.01 %
Rwork0.1941 --
obs0.1968 41320 90.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.503→49.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9228 0 1 70 9299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089403
X-RAY DIFFRACTIONf_angle_d1.02512716
X-RAY DIFFRACTIONf_dihedral_angle_d10.7355661
X-RAY DIFFRACTIONf_chiral_restr0.0541448
X-RAY DIFFRACTIONf_plane_restr0.0061618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5033-2.56150.31241430.24932506X-RAY DIFFRACTION88
2.5615-2.62560.31761360.23772661X-RAY DIFFRACTION93
2.6256-2.69660.32371420.23652672X-RAY DIFFRACTION93
2.6966-2.77590.30481350.22962636X-RAY DIFFRACTION93
2.7759-2.86550.28851490.22642649X-RAY DIFFRACTION92
2.8655-2.96790.34471200.22332645X-RAY DIFFRACTION92
2.9679-3.08670.28851290.22162650X-RAY DIFFRACTION92
3.0867-3.22720.23891320.21522657X-RAY DIFFRACTION92
3.2272-3.39730.2931370.20732603X-RAY DIFFRACTION91
3.3973-3.61010.25871180.20722625X-RAY DIFFRACTION90
3.6101-3.88870.21541360.18042597X-RAY DIFFRACTION89
3.8887-4.27980.24891670.17222574X-RAY DIFFRACTION89
4.2798-4.89860.20231300.16712610X-RAY DIFFRACTION88
4.8986-6.16990.23981330.1972573X-RAY DIFFRACTION87
6.1699-49.46030.21081620.17112593X-RAY DIFFRACTION84
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)
10.1642-0.15720.09830.2892-0.19760.9259-0.01630.1103-0.12020.05240.0437-0.00130.11430.0659-00.357-0.01130.02580.3802-0.01060.408729.070717.819540.7121
21.1294-0.0095-0.38310.8364-0.07550.79710.0611-0.00110.0686-0.0087-0.00290.0167-0.02950.0287-0.00010.3803-0.010.03830.3225-0.0350.354936.00641.269737.9639
30.91880.0752-0.17110.3706-0.05530.58790.08160.0801-0.14350.0243-0.05470.1425-0.0399-0.0034-00.3386-0.0025-0.00530.3753-0.04980.3251-2.581220.229511.6076
40.78410.1627-0.4020.3632-0.17930.49780.0756-0.031-0.0071-0.00640.00880.1259-0.03560.11980.00020.4303-0.01250.00120.41160.05820.39275.512442.576-7.0414
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 5 through 400)
2X-RAY DIFFRACTION2(chain 'B' and resid 6 through 328)
3X-RAY DIFFRACTION3(chain 'C' and resid 9 through 400)
4X-RAY DIFFRACTION4(chain 'D' and resid 2 through 160)

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