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- PDB-3rtr: A RING E3-substrate complex poised for ubiquitin-like protein tra... -

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Basic information

Entry
Database: PDB / ID: 3rtr
TitleA RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases
Components
  • Cullin-1
  • E3 ubiquitin-protein ligase RBX1
KeywordsLIGASE / UBIQUITIN / NEDD8 / CULLIN / UBL CONJUGATION PATHWAY / E3 LIGASE
Function / homology
Function and homology information


Parkin-FBXW7-Cul1 ubiquitin ligase complex / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / protein neddylation ...Parkin-FBXW7-Cul1 ubiquitin ligase complex / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / protein neddylation / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-ubiquitin ligase activity / Cul4A-RING E3 ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / negative regulation of type I interferon production / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / Cul3-RING ubiquitin ligase complex / Prolactin receptor signaling / protein monoubiquitination / cullin family protein binding / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / positive regulation of TORC1 signaling / Regulation of BACH1 activity / T cell activation / post-translational protein modification / MAP3K8 (TPL2)-dependent MAPK1/3 activation / intrinsic apoptotic signaling pathway / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Degradation of DVL / Recognition of DNA damage by PCNA-containing replication complex / Dectin-1 mediated noncanonical NF-kB signaling / cellular response to amino acid stimulus / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / animal organ morphogenesis / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / DNA Damage Recognition in GG-NER / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / G1/S transition of mitotic cell cycle / negative regulation of canonical Wnt signaling pathway / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / RING-type E3 ubiquitin transferase / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / NOTCH1 Intracellular Domain Regulates Transcription / Formation of TC-NER Pre-Incision Complex / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Formation of Incision Complex in GG-NER / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Interleukin-1 signaling / Dual incision in TC-NER / protein polyubiquitination / Orc1 removal from chromatin / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of RAS by GAPs / positive regulation of protein catabolic process / Regulation of RUNX2 expression and activity / cellular response to UV / Cyclin D associated events in G1 / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / Regulation of PLK1 Activity at G2/M Transition / MAPK cascade / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Circadian Clock / Downstream TCR signaling / Neddylation / ubiquitin-dependent protein catabolic process / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / cell population proliferation / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / molecular adaptor activity / protein ubiquitination / DNA repair / DNA damage response / ubiquitin protein ligase binding / zinc ion binding / nucleoplasm
Similarity search - Function
Cullin; Chain C, Domain 2 / Cullin Repeats / 5 helical Cullin repeat like / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin / Cullin repeat-like-containing domain superfamily ...Cullin; Chain C, Domain 2 / Cullin Repeats / 5 helical Cullin repeat like / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Ribosomal Protein S5; domain 2 / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Arc Repressor Mutant, subunit A / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / Cullin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsCalabrese, M.F. / Scott, D.C. / Duda, D.M. / Grace, C.R. / Kurinov, I. / Kriwacki, R.W. / Schulman, B.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases.
Authors: Calabrese, M.F. / Scott, D.C. / Duda, D.M. / Grace, C.R. / Kurinov, I. / Kriwacki, R.W. / Schulman, B.A.
History
DepositionMay 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references
Revision 1.2Sep 13, 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 / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cullin-1
B: E3 ubiquitin-protein ligase RBX1
C: Cullin-1
D: E3 ubiquitin-protein ligase RBX1
E: Cullin-1
F: E3 ubiquitin-protein ligase RBX1
G: Cullin-1
H: E3 ubiquitin-protein ligase RBX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,92020
Polymers219,1358
Non-polymers78512
Water0
1
G: Cullin-1
H: E3 ubiquitin-protein ligase RBX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9805
Polymers54,7842
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-20 kcal/mol
Surface area25040 Å2
MethodPISA
2
A: Cullin-1
B: E3 ubiquitin-protein ligase RBX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9805
Polymers54,7842
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-18 kcal/mol
Surface area24810 Å2
MethodPISA
3
C: Cullin-1
D: E3 ubiquitin-protein ligase RBX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9805
Polymers54,7842
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-12 kcal/mol
Surface area24270 Å2
MethodPISA
4
E: Cullin-1
F: E3 ubiquitin-protein ligase RBX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9805
Polymers54,7842
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-18 kcal/mol
Surface area25200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.475, 119.796, 231.861
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Cullin-1 / / CUL-1


Mass: 42694.035 Da / Num. of mol.: 4 / Fragment: UNP residues 411-776 / Mutation: L421E, V451E, V452K, Y455K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13616
#2: Protein
E3 ubiquitin-protein ligase RBX1 / Protein ZYP / RING finger protein 75 / RING-box protein 1 / Rbx1 / Regulator of cullins 1


Mass: 12089.677 Da / Num. of mol.: 4 / Fragment: UNP residues 5-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBX1, RNF75, ROC1 / Production host: Escherichia coli (E. coli)
References: UniProt: P62877, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn

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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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17% PEG 3350, 100 mM Tris pH 7.5, 200 mM Sodium/Postassium Tartrate, 2% Benzamidine Hydrochloride, 1% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.21→30 Å / Num. all: 41060 / Num. obs: 41039 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 101 Å2 / Rsym value: 0.059 / Net I/σ(I): 21.7

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LDJ

1ldj


Resolution: 3.21→29.949 Å / SU ML: 0.39 / σ(F): 1.35 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2825 2050 5 %
Rwork0.2377 --
obs-41038 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.821 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.7844 Å20 Å2-0 Å2
2--3.4204 Å20 Å2
3----9.2048 Å2
Refinement stepCycle: LAST / Resolution: 3.21→29.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14043 0 12 0 14055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714285
X-RAY DIFFRACTIONf_angle_d0.99219226
X-RAY DIFFRACTIONf_dihedral_angle_d15.3865379
X-RAY DIFFRACTIONf_chiral_restr0.0672148
X-RAY DIFFRACTIONf_plane_restr0.0042431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.21-3.32460.36242120.33313843X-RAY DIFFRACTION100
3.3246-3.45760.36922200.30623816X-RAY DIFFRACTION100
3.4576-3.61470.32741960.28943849X-RAY DIFFRACTION100
3.6147-3.80490.29521860.26083882X-RAY DIFFRACTION100
3.8049-4.04280.2662020.25223877X-RAY DIFFRACTION100
4.0428-4.3540.26472050.23693872X-RAY DIFFRACTION100
4.354-4.79060.27381870.22163903X-RAY DIFFRACTION100
4.7906-5.48010.26292190.22723903X-RAY DIFFRACTION100
5.4801-6.89050.30432090.24453953X-RAY DIFFRACTION100
6.8905-29.95030.23892140.18344090X-RAY DIFFRACTION99
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)
10.70760.3281-0.42451.36710.27662.279-0.0334-0.1507-0.00180.2077-0.35480.38360.2314-0.24390.29110.6433-0.00470.13490.7076-0.09330.7748-53.1322-4.815178.4034
21.0449-0.8891-0.41712.1455-0.68430.9445-0.0713-0.39610.087-0.12250.3986-0.7688-0.04080.4988-0.22070.6796-0.0118-0.04381.0203-0.13071.1228-12.27833.467170.5263
30.81840.2296-0.61731.0534-0.5912.25710.01450.04-0.1056-0.0368-0.0827-0.4749-0.42320.02170.06690.88450.03650.08610.8258-0.0440.9722-14.10095.829917.9625
41.3402-0.5430.93651.7276-1.22872.6688-0.0480.3376-0.1673-0.30780.04180.15890.1117-0.0157-0.05490.6046-0.0723-0.11530.61780.00890.5591-53.5027-15.565517.5848
50.84380.3597-1.03122.4863-0.18751.6574-0.039-0.27920.089-0.05120.0436-0.21810.03750.0827-0.01550.59320.03620.05660.6389-0.06980.728-34.777810.634770.0466
61.0055-1.53980.74091.833-0.65113.42950.0869-0.1022-0.425-0.4193-0.1192-0.26290.14680.10450.06360.44830.06330.02570.4279-0.02010.543-34.4-1.474760.6118
7-0.07230.7246-1.71843.0018-1.61272.34620.15710.26150.24180.23380.1451-0.0303-0.0973-0.1291-0.21010.4887-0.02930.00020.56780.05440.5744-33.9664-4.877931.0275
81.7987-0.04760.49531.23270.093-0.0313-0.02030.3128-0.2139-0.65210.1784-0.17720.2473-0.2819-0.03740.9883-0.11830.16290.8205-0.08260.7333-29.6924-15.05822.2548
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 411:776))
2X-RAY DIFFRACTION2chain 'C' and ((resseq 411:776))
3X-RAY DIFFRACTION3chain 'E' and ((resseq 411:776))
4X-RAY DIFFRACTION4chain 'G' and ((resseq 411:776))
5X-RAY DIFFRACTION5chain 'B' and ((resseq 5:108))
6X-RAY DIFFRACTION6chain 'D' and ((resseq 5:108))
7X-RAY DIFFRACTION7chain 'F' and ((resseq 5:108))
8X-RAY DIFFRACTION8chain 'H' and ((resseq 5:108))

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