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- PDB-9pwj: Fem-1 homolog B (FEM1B) in complex with VU0081201 -

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Basic information

Entry
Database: PDB / ID: 9pwj
TitleFem-1 homolog B (FEM1B) in complex with VU0081201
ComponentsProtein fem-1 homolog B
KeywordsLIGASE / FEM1B / E3 ligase / ligand
Function / homology
Function and homology information


regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / branching involved in prostate gland morphogenesis / regulation of DNA damage checkpoint / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of extrinsic apoptotic signaling pathway via death domain receptors / death receptor binding / Cul2-RING ubiquitin ligase complex / ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity ...regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / branching involved in prostate gland morphogenesis / regulation of DNA damage checkpoint / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of extrinsic apoptotic signaling pathway via death domain receptors / death receptor binding / Cul2-RING ubiquitin ligase complex / ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / apoptotic process / mitochondrion / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
: / Protein fem-1 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKatinas, J.M. / Fesik, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateArvinas Inc. research agreement AWD00000788 United States
CitationJournal: Protein Sci. / Year: 2025
Title: Nuclear Magnetic Resonance-based fragment screen of the E3 ligase Fem-1 homolog B.
Authors: Katinas, J.M. / Amporndanai, K. / Taylor, A.J. / Rose, K.L. / Gareiss, P.C. / Crespo, R.A. / Phan, J. / Waterson, A.G. / Fesik, S.W.
History
DepositionAug 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein fem-1 homolog B
B: Protein fem-1 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2778
Polymers78,5922
Non-polymers6866
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.544, 128.544, 139.751
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein Protein fem-1 homolog B / FEM1b / FEM1-beta / Fem-1-like death receptor-binding protein alpha / Fem-1-like in apoptotic ...FEM1b / FEM1-beta / Fem-1-like death receptor-binding protein alpha / Fem-1-like in apoptotic pathway protein alpha / F1A-alpha


Mass: 39295.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FEM1B, F1AA, KIAA0396 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UK73
#2: Chemical ChemComp-A1CL1 / 3-(2-oxopyrrolidin-1-yl)benzoic acid


Mass: 205.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.67 Å3/Da / Density % sol: 66.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.25% PEG 8000, 1.2 M-1.6 M ammonium sulfate, and 0.05-0.1 M sodium thiocyanate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Dec 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→47.3 Å / Num. obs: 40783 / % possible obs: 99.7 % / Redundancy: 11.1 % / Biso Wilson estimate: 73.57 Å2 / CC1/2: 0.984 / Net I/σ(I): 9.4
Reflection shellResolution: 3→3.18 Å / Num. unique obs: 40783 / CC1/2: 0.317

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→47.3 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.6303
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3469 1155 4.87 %
Rwork0.2962 22548 -
obs0.2986 23703 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.75 Å2
Refinement stepCycle: LAST / Resolution: 3→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4969 0 40 3 5012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035104
X-RAY DIFFRACTIONf_angle_d0.58826950
X-RAY DIFFRACTIONf_chiral_restr0.0375805
X-RAY DIFFRACTIONf_plane_restr0.0064907
X-RAY DIFFRACTIONf_dihedral_angle_d4.9802747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.140.45751420.42012790X-RAY DIFFRACTION98.95
3.14-3.30.41771660.36672764X-RAY DIFFRACTION99.36
3.3-3.510.44791740.38112762X-RAY DIFFRACTION98.99
3.51-3.780.43441330.36662771X-RAY DIFFRACTION97.71
3.78-4.160.35871360.32762762X-RAY DIFFRACTION97.35
4.16-4.760.351090.26572833X-RAY DIFFRACTION97.68
4.76-60.31441580.26812841X-RAY DIFFRACTION98.75
6-47.30.23331370.22133025X-RAY DIFFRACTION97.83

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