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- PDB-9pq9: Fem-1 homolog B (FEM1B) in complex with VU0421763 -

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Basic information

Entry
Database: PDB / ID: 9pq9
TitleFem-1 homolog B (FEM1B) in complex with VU0421763
ComponentsProtein fem-1 homolog B
KeywordsLIGASE / FEM1B / E3 ligase
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: 2.93 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)79,4929
Polymers78,5922
Non-polymers9017
Water00
1
A: Protein fem-1 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6023
Polymers39,2961
Non-polymers3062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein fem-1 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8906
Polymers39,2961
Non-polymers5955
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.435, 124.435, 138.638
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 and (name N or name...
d_2ens_1(chain "B" and (resid 0 through 134 or (resid 135...

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_11HISHISASPASPAA0 - 2861 - 287
d_12ILEILEGLYGLYAA290 - 337289 - 336
d_13V17V17V17V17AC401
d_21HISHISGLYGLYBB0 - 3371 - 335
d_22V17V17V17V17BD401

NCS oper: (Code: givenMatrix: (-0.295017419665, 0.955451135086, -0.00882329630934), (0.955015394747, 0.294566139005, -0.0342984773566), (-0.030171474795, -0.018545032096, -0.999372685185)Vector: 80. ...NCS oper: (Code: given
Matrix: (-0.295017419665, 0.955451135086, -0.00882329630934), (0.955015394747, 0.294566139005, -0.0342984773566), (-0.030171474795, -0.018545032096, -0.999372685185)
Vector: 80.6154268163, -57.9698717076, 69.259259643)

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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-A1CI7 / 6-(propylsulfanyl)-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one


Mass: 210.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10N4OS / 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
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: 3.41 Å3/Da / Density % sol: 63.98 %
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→46.3 Å / Num. obs: 93515 / % possible obs: 100 % / Redundancy: 26 % / Biso Wilson estimate: 70.33 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 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.93→46.3 Å / SU ML: 0.4859 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.103
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3036 1170 4.92 %
Rwork0.2587 22591 -
obs0.2609 23761 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.63 Å2
Refinement stepCycle: LAST / Resolution: 2.93→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5018 0 53 0 5071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00425155
X-RAY DIFFRACTIONf_angle_d0.80227012
X-RAY DIFFRACTIONf_chiral_restr0.0467818
X-RAY DIFFRACTIONf_plane_restr0.0049908
X-RAY DIFFRACTIONf_dihedral_angle_d17.4731806
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.905739520187 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.93-3.060.36751380.35282805X-RAY DIFFRACTION99.93
3.06-3.220.37191410.32672797X-RAY DIFFRACTION99.83
3.22-3.430.36831550.33052792X-RAY DIFFRACTION99.97
3.43-3.690.38551550.30212777X-RAY DIFFRACTION98.85
3.69-4.060.34491200.26872800X-RAY DIFFRACTION97.95
4.06-4.650.2891510.23912752X-RAY DIFFRACTION96.57
4.65-5.860.28371610.25052827X-RAY DIFFRACTION98.1
5.86-46.30.23221490.20383041X-RAY DIFFRACTION99.16

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