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- PDB-8caf: N8C_Fab3b in complex with NEDD8-CUL1(WHB) -

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Basic information

Entry
Database: PDB / ID: 8caf
TitleN8C_Fab3b in complex with NEDD8-CUL1(WHB)
Components
  • Cullin-1
  • Fab Heavy Chain
  • Fab Light Chain
  • NEDD8
KeywordsCELL CYCLE / NEDD8 / Cullin-RING ligase / ubiquitin / antibody
Function / homology
Function and homology information


Parkin-FBXW7-Cul1 ubiquitin ligase complex / cullin-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / protein neddylation / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling / TGF-beta receptor signaling activates SMADs / regulation of postsynapse assembly ...Parkin-FBXW7-Cul1 ubiquitin ligase complex / cullin-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / protein neddylation / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling / TGF-beta receptor signaling activates SMADs / regulation of postsynapse assembly / regulation of proteolysis / anatomical structure morphogenesis / protein monoubiquitination / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / intrinsic apoptotic signaling pathway / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / animal organ morphogenesis / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Iron uptake and transport / Negative regulation of NOTCH4 signaling / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / protein modification process / Degradation of beta-catenin by the destruction complex / modification-dependent protein catabolic process / NOTCH1 Intracellular Domain Regulates Transcription / 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 / G1/S transition of mitotic cell cycle / FCERI mediated NF-kB activation / protein tag activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / UCH proteinases / : / Regulation of PLK1 Activity at G2/M Transition / intracellular protein localization / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / cell population proliferation / protein ubiquitination / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / glutamatergic synapse / proteolysis / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Nedd8-like ubiquitin / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin / Cullin, N-terminal ...Nedd8-like ubiquitin / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Roll / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cullin-1 / Ubiquitin-like protein NEDD8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsDuda, D.M. / Yanishevski, D. / Henneberg, L.T. / Schulman, B.A.
Funding support United States, European Union, Germany, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA021765 United States
European Research Council (ERC)ADG-789016-Nedd8ActivateEuropean Union
Max Planck Society Germany
German Research Foundation (DFG)SCHU3196/1-1 Germany
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: Activity-based profiling of cullin-RING E3 networks by conformation-specific probes.
Authors: Henneberg, L.T. / Singh, J. / Duda, D.M. / Baek, K. / Yanishevski, D. / Murray, P.J. / Mann, M. / Sidhu, S.S. / Schulman, B.A.
History
DepositionJan 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab Light Chain
B: Fab Heavy Chain
C: Fab Light Chain
D: Fab Heavy Chain
E: Cullin-1
F: NEDD8
G: NEDD8
H: Cullin-1


Theoretical massNumber of molelcules
Total (without water)128,5318
Polymers128,5318
Non-polymers00
Water00
1
A: Fab Light Chain
B: Fab Heavy Chain
F: NEDD8
H: Cullin-1


Theoretical massNumber of molelcules
Total (without water)64,2664
Polymers64,2664
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Fab Light Chain
D: Fab Heavy Chain
E: Cullin-1
G: NEDD8


Theoretical massNumber of molelcules
Total (without water)64,2664
Polymers64,2664
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.372, 106.871, 180.651
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Antibody Fab Light Chain


Mass: 22958.494 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli K-12 (bacteria)
#2: Antibody Fab Heavy Chain


Mass: 23391.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli K-12 (bacteria)
#3: Protein Cullin-1 / CUL-1


Mass: 9341.104 Da / Num. of mol.: 2 / Fragment: UNP residues 677-776
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q13616
#4: Protein NEDD8 / Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / ...Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / Ubiquitin-like protein Nedd8


Mass: 8573.978 Da / Num. of mol.: 2 / Fragment: UNP residues 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q15843
Has protein modificationY

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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: 3.64 Å3/Da / Density % sol: 66.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.0-2.1M Ammonium Sulfate, 0.1M Citrate pH 6.0, 10mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.66→180 Å / Num. obs: 56730 / % possible obs: 98.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 77.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 23.8
Reflection shellResolution: 2.66→2.74 Å / Rmerge(I) obs: 1.165 / Num. unique obs: 4609 / CC1/2: 0.612

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDSVersion November 3, 2014data reduction
Aimlessdata scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→90.33 Å / SU ML: 0.461 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4446
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.263 2874 5.07 %
Rwork0.2166 53775 -
obs0.2189 56649 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.51 Å2
Refinement stepCycle: LAST / Resolution: 2.66→90.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8808 0 0 0 8808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00948978
X-RAY DIFFRACTIONf_angle_d1.177412173
X-RAY DIFFRACTIONf_chiral_restr0.06221404
X-RAY DIFFRACTIONf_plane_restr0.011541
X-RAY DIFFRACTIONf_dihedral_angle_d6.91541240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.70.46651470.4382491X-RAY DIFFRACTION98.84
2.7-2.750.41371370.36412561X-RAY DIFFRACTION98.18
2.75-2.80.41811290.32642507X-RAY DIFFRACTION98.47
2.8-2.850.32881380.28422480X-RAY DIFFRACTION95.69
2.85-2.910.30411210.25092539X-RAY DIFFRACTION98.63
2.91-2.980.31161450.25742519X-RAY DIFFRACTION98.63
2.98-3.040.33531370.28392575X-RAY DIFFRACTION99.3
3.04-3.120.34751430.30332566X-RAY DIFFRACTION99.49
3.12-3.210.42321430.31112543X-RAY DIFFRACTION99.08
3.21-3.30.33891400.29432564X-RAY DIFFRACTION99.12
3.3-3.410.28261280.25062563X-RAY DIFFRACTION99.01
3.41-3.530.2641200.2222463X-RAY DIFFRACTION94.44
3.53-3.670.25521340.21382563X-RAY DIFFRACTION99.01
3.67-3.840.28811220.22542585X-RAY DIFFRACTION98.94
3.84-4.040.25261530.21712571X-RAY DIFFRACTION99.56
4.04-4.290.23051450.18652591X-RAY DIFFRACTION98.99
4.29-4.620.20511610.16742502X-RAY DIFFRACTION96.28
4.62-5.090.22951340.16172620X-RAY DIFFRACTION99.21
5.09-5.820.23291360.18712627X-RAY DIFFRACTION99.46
5.82-7.330.26871300.21512590X-RAY DIFFRACTION96.22
7.34-90.330.2181310.19542755X-RAY DIFFRACTION97.5

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