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- PDB-9pw8: Fem-1 homolog B (FEM1B) in complex with VU0417412 -

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Basic information

Entry
Database: PDB / ID: 9pw8
TitleFem-1 homolog B (FEM1B) in complex with VU0417412
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: 2.8 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)79,0344
Polymers78,5922
Non-polymers4432
Water00
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)123.708, 123.708, 137.786
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 0 through 203 or (resid 204...
d_2ens_1(chain "B" and (resid 0 through 243 or resid 247...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11HISHISGLYGLYAA0 - 3372 - 339
d_12V74V74V74V74AC401
d_21HISHISASPASPBB0 - 2432 - 245
d_22ARGARGGLYGLYBB247 - 337249 - 339
d_23V74V74V74V74BD401

NCS oper: (Code: givenMatrix: (-0.27443363859, 0.961588966301, 0.00573043607699), (0.961537330899, 0.274480394362, -0.0103186432842), (-0.0114951858836, 0.00267824538856, -0.999930341425)Vector: 79. ...NCS oper: (Code: given
Matrix: (-0.27443363859, 0.961588966301, 0.00573043607699), (0.961537330899, 0.274480394362, -0.0103186432842), (-0.0114951858836, 0.00267824538856, -0.999930341425)
Vector: 79.0005784784, -59.2543222728, 68.7644751731)

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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-A1CLY / N-(4-fluorophenyl)thiophene-2-carboxamide


Mass: 221.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H8FNOS / Feature type: SUBJECT OF INVESTIGATION
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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.25% PEG 8000, 1.2-1.6 M Ammonium sulfate, 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 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.73→46.03 Å / Num. obs: 755781 / % possible obs: 100 % / Redundancy: 26 % / Biso Wilson estimate: 62.08 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.6
Reflection shellResolution: 2.73→2.86 Å / Num. unique obs: 93515 / CC1/2: 0.368

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→46.03 Å / SU ML: 0.6778 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 43.8484
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3378 2514 5.01 %
Rwork0.2994 47667 -
obs0.3014 50181 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.29 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5004 0 30 0 5034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00655118
X-RAY DIFFRACTIONf_angle_d1.21396953
X-RAY DIFFRACTIONf_chiral_restr0.0773817
X-RAY DIFFRACTIONf_plane_restr0.0143908
X-RAY DIFFRACTIONf_dihedral_angle_d7.3716749
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.03078857704 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.850.44581200.43422684X-RAY DIFFRACTION99.36
2.85-2.910.43871350.40182643X-RAY DIFFRACTION99.93
2.91-2.980.45371060.40892697X-RAY DIFFRACTION99.82
2.98-3.040.42971480.39822624X-RAY DIFFRACTION99.86
3.04-3.120.4331720.40542625X-RAY DIFFRACTION99.61
3.12-3.210.44881490.38752613X-RAY DIFFRACTION99.64
3.21-3.30.38991250.37762688X-RAY DIFFRACTION99.93
3.3-3.410.39271140.37132667X-RAY DIFFRACTION99.86
3.41-3.530.391500.35392643X-RAY DIFFRACTION99.68
3.53-3.670.4221230.34742651X-RAY DIFFRACTION99.71
3.67-3.840.35851330.32422664X-RAY DIFFRACTION99.43
3.84-4.040.35971440.28912620X-RAY DIFFRACTION99.28
4.04-4.290.35051450.27772659X-RAY DIFFRACTION99.19
4.29-4.620.30681490.26592599X-RAY DIFFRACTION99.46
4.62-5.090.30121570.26232634X-RAY DIFFRACTION99.61
5.09-5.820.36411520.27392646X-RAY DIFFRACTION99.79
5.82-7.330.22921380.26572665X-RAY DIFFRACTION100
7.33-46.030.25421540.20212645X-RAY DIFFRACTION99.79

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