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- PDB-9pxo: Fem-1 homolog B (FEM1B) in complex with VU0023775 -

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Basic information

Entry
Database: PDB / ID: 9pxo
TitleFem-1 homolog B (FEM1B) in complex with VU0023775
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: 3.05 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 6, 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)79,0864
Polymers78,5922
Non-polymers4942
Water00
1
A: Protein fem-1 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5432
Polymers39,2961
Non-polymers2471
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein fem-1 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5432
Polymers39,2961
Non-polymers2471
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.844, 129.844, 139.967
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 25 or (resid 26...
d_2ens_1(chain "B" and (resid 0 through 304 or (resid 305...

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_11HISHISLEULEUAA0 - 3361 - 335
d_12V37V37V37V37AC403
d_21HISHISLEULEUBB0 - 3362 - 336
d_22V37V37V37V37BD403

NCS oper: (Code: givenMatrix: (0.390332387082, -0.919878797351, 0.038257362412), (-0.920674004239, -0.38999859708, 0.0161391509879), (7.42548676095E-5, -0.041522192374, -0.999137579128)Vector: -40. ...NCS oper: (Code: given
Matrix: (0.390332387082, -0.919878797351, 0.038257362412), (-0.920674004239, -0.38999859708, 0.0161391509879), (7.42548676095E-5, -0.041522192374, -0.999137579128)
Vector: -40.6795960461, -60.6541979257, 68.0640502904)

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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-A1CMX / 2-tert-butyl-1,3-dioxo-2,3-dihydro-1H-isoindole-5-carboxylic acid


Mass: 247.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H13NO4 / 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: 3.75 Å3/Da / Density % sol: 67.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M 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: 3.05→47.6 Å / Num. obs: 52680 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 89.52 Å2 / CC1/2: 0.997 / Net I/σ(I): 14.1
Reflection shellResolution: 3.05→3.26 Å / Redundancy: 12.6 % / Num. unique obs: 52680 / CC1/2: 0.432 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→47.6 Å / SU ML: 0.7835 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 42.9078
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3397 2378 5.56 %
Rwork0.2847 40363 -
obs0.2879 42741 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.24 Å2
Refinement stepCycle: LAST / Resolution: 3.05→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4996 0 36 0 5032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00475116
X-RAY DIFFRACTIONf_angle_d1.03596964
X-RAY DIFFRACTIONf_chiral_restr0.0563820
X-RAY DIFFRACTIONf_plane_restr0.0069909
X-RAY DIFFRACTIONf_dihedral_angle_d5.591749
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.08470781373 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.110.51611800.48722192X-RAY DIFFRACTION92.44
3.11-3.180.45581390.45062401X-RAY DIFFRACTION98.49
3.18-3.250.4031430.4032402X-RAY DIFFRACTION98.83
3.25-3.340.4521400.38692411X-RAY DIFFRACTION99.65
3.34-3.430.42791250.38312410X-RAY DIFFRACTION99.02
3.43-3.530.47341550.43172093X-RAY DIFFRACTION88.36
3.53-3.640.43051030.35562439X-RAY DIFFRACTION99.53
3.64-3.770.46981340.42632372X-RAY DIFFRACTION97.51
3.77-3.920.45591150.40022380X-RAY DIFFRACTION97.01
3.92-4.10.34541430.30692368X-RAY DIFFRACTION98.39
4.1-4.310.29781530.26282384X-RAY DIFFRACTION99.18
4.32-4.590.31421450.25732398X-RAY DIFFRACTION99.45
4.59-4.940.32171480.23152402X-RAY DIFFRACTION99.49
4.94-5.440.33161510.24552419X-RAY DIFFRACTION99.77
5.44-6.220.3321510.24672404X-RAY DIFFRACTION99.8
6.22-7.830.2882840.22482472X-RAY DIFFRACTION99.88
7.83-47.60.22771690.17392416X-RAY DIFFRACTION99.77
Refinement TLS params.Method: refined / Origin x: -29.526983178 Å / Origin y: -23.2919817401 Å / Origin z: 34.854033271 Å
111213212223313233
T0.509761905042 Å20.101489543009 Å20.00246218931033 Å2-0.641465662485 Å2-0.130401750883 Å2--0.572892173807 Å2
L1.64007814926 °20.529312694647 °2-0.703915079543 °2-1.05602983514 °2-0.535684920065 °2--0.765251673793 °2
S0.00503277158881 Å °0.383443947709 Å °-0.241906849831 Å °-0.213627740098 Å °0.0632621771843 Å °-0.304299473385 Å °-0.00872796288551 Å °-0.0201323716126 Å °-0.0557730096249 Å °
Refinement TLS groupSelection details: all

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