[English] 日本語
Yorodumi
- PDB-5vzu: Crystal structure of the Skp1-FBXO31-cyclin D1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vzu
TitleCrystal structure of the Skp1-FBXO31-cyclin D1 complex
Components
  • Cyclin D1
  • F-box only protein 31
  • S-phase kinase-associated protein 1
KeywordsCELL CYCLE / ubiquitin ligase
Function / homology
Function and homology information


cyclin D1-CDK4 complex / cyclin D1-CDK6 complex / re-entry into mitotic cell cycle / Drug-mediated inhibition of CDK4/CDK6 activity / RUNX3 regulates WNT signaling / positive regulation of mammary gland epithelial cell proliferation / response to leptin / F-box domain binding / anaphase-promoting complex-dependent catabolic process / Transcriptional regulation by RUNX2 ...cyclin D1-CDK4 complex / cyclin D1-CDK6 complex / re-entry into mitotic cell cycle / Drug-mediated inhibition of CDK4/CDK6 activity / RUNX3 regulates WNT signaling / positive regulation of mammary gland epithelial cell proliferation / response to leptin / F-box domain binding / anaphase-promoting complex-dependent catabolic process / Transcriptional regulation by RUNX2 / Leydig cell differentiation / PcG protein complex / maintenance of protein location in nucleus / Cul7-RING ubiquitin ligase complex / proline-rich region binding / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / cyclin-dependent protein serine/threonine kinase activator activity / Regulation of RUNX1 Expression and Activity / response to iron ion / ubiquitin ligase activator activity / mammary gland epithelial cell proliferation / cyclin-dependent protein serine/threonine kinase regulator activity / response to UV-A / response to vitamin E / SCF ubiquitin ligase complex / negative regulation of epithelial cell differentiation / response to corticosterone / PTK6 Regulates Cell Cycle / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / ubiquitin ligase complex scaffold activity / Transcriptional Regulation by VENTX / microtubule organizing center / mammary gland alveolus development / RUNX3 regulates p14-ARF / response to magnesium ion / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / bicellular tight junction / cullin family protein binding / positive regulation of G2/M transition of mitotic cell cycle / response to X-ray / protein monoubiquitination / positive regulation of G1/S transition of mitotic cell cycle / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / fat cell differentiation / cyclin-dependent protein kinase holoenzyme complex / ubiquitin-like ligase-substrate adaptor activity / mitotic G1 DNA damage checkpoint signaling / signal transduction in response to DNA damage / Nuclear events stimulated by ALK signaling in cancer / endoplasmic reticulum unfolded protein response / lactation / transcription repressor complex / protein K48-linked ubiquitination / liver regeneration / cyclin binding / molecular function activator activity / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / protein serine/threonine kinase activator activity / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of CRY and PER proteins / G1/S transition of mitotic cell cycle / Activation of NF-kappaB in B cells / Iron uptake and transport / Degradation of GLI1 by the proteasome / 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 / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / response to calcium ion / response to estrogen / beta-catenin binding / Degradation of beta-catenin by the destruction complex / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / CLEC7A (Dectin-1) signaling / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / histone deacetylase binding / Wnt signaling pathway / RMTs methylate histone arginines / neuron differentiation / Interleukin-1 signaling / Orc1 removal from chromatin / protein polyubiquitination / Cyclin D associated events in G1 / Regulation of RUNX2 expression and activity / transcription corepressor activity / Regulation of PLK1 Activity at G2/M Transition / response to estradiol
Similarity search - Function
F-box only protein 31/39 / Cyclin D1 binding domain / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain ...F-box only protein 31/39 / Cyclin D1 binding domain / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Cyclin, N-terminal / Cyclin, N-terminal domain / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / SKP1/BTB/POZ domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / G1/S-specific cyclin-D1 / S-phase kinase-associated protein 1 / F-box only protein 31 / Cyclin D1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi, Y. / Jin, K. / Hao, B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM099948 United States
Connecticut Regenerative Medicine Research Fund15-RMA-UCHC-04 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis of the phosphorylation-independent recognition of cyclin D1 by the SCFFBXO31 ubiquitin ligase.
Authors: Li, Y. / Jin, K. / Bunker, E. / Zhang, X. / Luo, X. / Liu, X. / Hao, B.
History
DepositionMay 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: S-phase kinase-associated protein 1
B: F-box only protein 31
C: S-phase kinase-associated protein 1
D: F-box only protein 31
E: Cyclin D1
F: Cyclin D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,13718
Polymers149,0576
Non-polymers1,08112
Water1,11762
1
A: S-phase kinase-associated protein 1
B: F-box only protein 31
E: Cyclin D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0699
Polymers74,5283
Non-polymers5406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: S-phase kinase-associated protein 1
D: F-box only protein 31
F: Cyclin D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0699
Polymers74,5283
Non-polymers5406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.679, 156.235, 155.522
Angle α, β, γ (deg.)90.000, 104.210, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21C
12B
22D
13E
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1010 - 1066
2115C1010 - 1066
1215A1083 - 1160
2215C1083 - 1160
1125B12 - 203
2125D12 - 203
1225B220 - 487
2225D220 - 487
1133E288 - 293
2133F288 - 293

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.163247, 0.0554, -0.985029), (0.070896, -0.9965, -0.044296), (-0.984035, -0.062604, -0.166603)-21.04232, -0.63435, 76.774117

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: 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: 16827.127 Da / Num. of mol.: 2 / Mutation: P2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63208
#2: Protein F-box only protein 31


Mass: 55730.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBXO31, FBX14, FBX31, PP2386
Details (production host): modified pET15b vector with a StrepII tag
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5XUX0

-
Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide Cyclin D1


Mass: 1971.019 Da / Num. of mol.: 2 / Fragment: UNP residues 109-125 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H014, UniProt: P24385*PLUS

-
Non-polymers , 3 types, 74 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationN
Sequence detailsresidues 38-43 deleted, residues 70-83 replaced with GGSGT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 100 mM sodium citrate (pH 5.3), 0.27 M ammonium acetate, 13-17% MPD, 0.02 M CaCl2
PH range: 5.3-5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2014 / Details: Mini-gap Undulator
RadiationMonochromator: Striped mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 55014 / % possible obs: 99.1 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.059 / Χ2: 0.906 / Net I/σ(I): 9.7 / Num. measured all: 416593
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
2.7-2.756.60.6960.712190.9
2.75-2.86.90.6330.722194.5
2.8-2.857.10.5970.74198
2.85-2.917.40.4780.747199.9
2.91-2.977.60.3850.7531100
2.97-3.047.70.3220.7741100
3.04-3.127.70.2590.7921100
3.12-3.27.70.2010.7721100
3.2-3.37.70.1510.8111100
3.3-3.47.70.1270.8331100
3.4-3.527.80.0940.841100
3.52-3.667.70.0790.8641100
3.66-3.837.80.0630.8921100
3.83-4.037.70.0560.9771100
4.03-4.297.70.0511.2431100
4.29-4.627.70.0511.2231100
4.62-5.087.70.0461.1041100
5.08-5.817.70.0391.0491100
5.81-7.327.70.0361.0711100
7.32-507.60.0271.095198.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VZT

5vzt


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 22.513 / SU ML: 0.214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.394 / ESU R Free: 0.272 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2674 4.9 %RANDOM
Rwork0.1804 ---
obs0.1829 52339 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 238.66 Å2 / Biso mean: 89.949 Å2 / Biso min: 24.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å2-0 Å2-1.36 Å2
2---1.77 Å20 Å2
3---1.47 Å2
Refinement stepCycle: final / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9191 0 52 62 9305
Biso mean--116.35 62.79 -
Num. residues----1138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199519
X-RAY DIFFRACTIONr_bond_other_d0.0010.029005
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.96312885
X-RAY DIFFRACTIONr_angle_other_deg0.802320728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65651143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22323.521463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.676151661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3711578
X-RAY DIFFRACTIONr_chiral_restr0.080.21391
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110645
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022221
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A794MEDIUM POSITIONAL0.260.5
1A1350LOOSE POSITIONAL0.415
1A794MEDIUM THERMAL15.262
1A1350LOOSE THERMAL15.4210
2B2337MEDIUM POSITIONAL0.280.5
2B4029LOOSE POSITIONAL0.385
2B2337MEDIUM THERMAL7.542
2B4029LOOSE THERMAL8.4310
3E64LOOSE POSITIONAL0.695
3E35TIGHT THERMAL17.490.5
3E64LOOSE THERMAL10.7810
LS refinement shellResolution: 2.702→2.772 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 198 -
Rwork0.3 3507 -
all-3705 -
obs--90.88 %
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)
13.35810.51121.38371.4381-0.07961.76940.05920.2990.3525-0.1562-0.2193-0.0859-0.03220.26850.16010.04360.02970.03660.08820.04650.0958-2.7414-26.963158.1962
21.0871-1.75490.27972.9129-0.42630.3636-0.1073-0.0350.08790.23970.1409-0.142-0.077-0.0274-0.03360.15060.0488-0.06360.10660.04950.1429-42.6631-2.758256.3568
31.97360.18321.22252.03250.6383.9686-0.33551.1404-0.1013-0.04310.2031-0.1714-0.36631.77810.13250.4884-0.3936-0.24721.08890.12550.216619.324128.4883-14.0605
41.7551-0.23610.73861.389-1.15193.2226-0.00440.4564-0.4644-0.6512-0.07240.4220.39410.21640.07690.40110.0644-0.2070.1991-0.13710.366315.95212.867225.6754
53.96483.9601-7.01753.9809-7.018412.42930.3680.53540.40610.38150.42320.4259-0.7119-0.9274-0.79120.2190.11070.08180.34450.05070.2745-59.811117.534352.6676
69.39629.3217-7.885713.8795-14.205115.42470.0158-1.24990.2848-0.60950.03930.120.8061-0.7419-0.05510.297-0.07490.06340.5788-0.01730.239420.712-17.050141.4879
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1008 - 1163
2X-RAY DIFFRACTION2B63 - 539
3X-RAY DIFFRACTION3C1008 - 1163
4X-RAY DIFFRACTION4D64 - 539
5X-RAY DIFFRACTION5E287 - 293
6X-RAY DIFFRACTION6F290 - 293

+
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