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- PDB-9pqe: Fem-1 homolog B (FEM1B) in complex with VU0412674 -

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Basic information

Entry
Database: PDB / ID: 9pqe
TitleFem-1 homolog B (FEM1B) in complex with VU0412674
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 / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of DNA damage checkpoint / 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 / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of DNA damage checkpoint / 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: 3.1 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
DepositionJul 22, 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)79,0744
Polymers78,5922
Non-polymers4832
Water724
1
A: Protein fem-1 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5372
Polymers39,2961
Non-polymers2411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein fem-1 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5372
Polymers39,2961
Non-polymers2411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.015, 130.015, 140.431
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 1 through 15 or (resid 16...
d_2ens_1(chain "B" and (resid 1 through 151 or (resid 152...

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_11METMETASPASPAA1 - 2862 - 287
d_12LEULEUGLYGLYAA291 - 337290 - 336
d_13V26V26V26V26AC403
d_21METMETGLYGLYBB1 - 3371 - 333
d_22V26V26V26V26BD403

NCS oper: (Code: givenMatrix: (0.403417276053, -0.913286607193, -0.0562323261511), (-0.914552462375, -0.404406874111, 0.0069909752988), (-0.0291255033544, 0.0486071321346, -0.998393235033)Vector: -57. ...NCS oper: (Code: given
Matrix: (0.403417276053, -0.913286607193, -0.0562323261511), (-0.914552462375, -0.404406874111, 0.0069909752988), (-0.0291255033544, 0.0486071321346, -0.998393235033)
Vector: -57.3836793725, -91.0800281756, 70.6596521782)

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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-A1CI9 / N-[4-(propan-2-yl)phenyl]pyrazine-2-carboxamide


Mass: 241.288 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.78 Å3/Da / Density % sol: 67.42 %
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: 3.1→47.7 Å / Num. obs: 53159 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 100.76 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.1
Reflection shellResolution: 3.1→3.31 Å / Num. unique obs: 53159 / CC1/2: 0.405

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→47.7 Å / SU ML: 0.7312 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.465
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3259 1105 4.95 %
Rwork0.2604 21197 -
obs0.264 22302 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.24 Å2
Refinement stepCycle: LAST / Resolution: 3.1→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5138 0 36 4 5178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01035265
X-RAY DIFFRACTIONf_angle_d1.3097145
X-RAY DIFFRACTIONf_chiral_restr0.0596819
X-RAY DIFFRACTIONf_plane_restr0.0114928
X-RAY DIFFRACTIONf_dihedral_angle_d17.40741877
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.58214671863 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.240.44521560.3812575X-RAY DIFFRACTION99.64
3.24-3.410.43831370.36552590X-RAY DIFFRACTION99.38
3.41-3.620.40211050.35922645X-RAY DIFFRACTION99.49
3.63-3.910.42611150.31942613X-RAY DIFFRACTION98.06
3.91-4.30.32181150.26752625X-RAY DIFFRACTION98.99
4.3-4.920.33471320.25312657X-RAY DIFFRACTION99.11
4.92-6.20.33231610.25322681X-RAY DIFFRACTION99.51
6.2-47.70.26571840.19672811X-RAY DIFFRACTION99.7

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