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- PDB-6wjh: Crystal structure of MAGE-A11 bound to the PCF11 degron -

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Basic information

Entry
Database: PDB / ID: 6wjh
TitleCrystal structure of MAGE-A11 bound to the PCF11 degron
ComponentsFusion protein of PCF11 and MAGE-A11
KeywordsLIGASE / MAGE-A11 / PCF 11 / ubiquitin ligase / protein complex
Function / homology
Function and homology information


: / mRNA cleavage factor complex / Processing of Intronless Pre-mRNAs / mRNA 3'-end processing / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / : / termination of RNA polymerase II transcription / RNA polymerase II complex binding / RNA polymerase II transcribes snRNA genes ...: / mRNA cleavage factor complex / Processing of Intronless Pre-mRNAs / mRNA 3'-end processing / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / : / termination of RNA polymerase II transcription / RNA polymerase II complex binding / RNA polymerase II transcribes snRNA genes / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / nuclear body / mRNA binding / mitochondrion / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Melanoma-associated antigen 11 / Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain ...Melanoma-associated antigen 11 / Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS
Similarity search - Domain/homology
Pre-mRNA cleavage complex 2 protein Pcf11 / Melanoma-associated antigen 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.19 Å
AuthorsMiller, D.J. / Huang, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)181691010 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for substrate recognition and chemical inhibition of oncogenic MAGE ubiquitin ligases.
Authors: Yang, S.W. / Huang, X. / Lin, W. / Min, J. / Miller, D.J. / Mayasundari, A. / Rodrigues, P. / Griffith, E.C. / Gee, C.T. / Li, L. / Li, W. / Lee, R.E. / Rankovic, Z. / Chen, T. / Potts, P.R.
History
DepositionApr 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion protein of PCF11 and MAGE-A11
B: Fusion protein of PCF11 and MAGE-A11
C: Fusion protein of PCF11 and MAGE-A11
D: Fusion protein of PCF11 and MAGE-A11


Theoretical massNumber of molelcules
Total (without water)111,2034
Polymers111,2034
Non-polymers00
Water3,747208
1
A: Fusion protein of PCF11 and MAGE-A11


Theoretical massNumber of molelcules
Total (without water)27,8011
Polymers27,8011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fusion protein of PCF11 and MAGE-A11


Theoretical massNumber of molelcules
Total (without water)27,8011
Polymers27,8011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fusion protein of PCF11 and MAGE-A11


Theoretical massNumber of molelcules
Total (without water)27,8011
Polymers27,8011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fusion protein of PCF11 and MAGE-A11


Theoretical massNumber of molelcules
Total (without water)27,8011
Polymers27,8011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.493, 78.195, 72.911
Angle α, β, γ (deg.)77.440, 77.340, 89.590
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Fusion protein of PCF11 and MAGE-A11 / / Pre-mRNA cleavage complex II protein Pcf11 / Cancer/testis antigen 1.11 / CT1.11 / MAGE-11 antigen


Mass: 27800.822 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCF11, KIAA0824, MAGEA11, MAGE11 / Production host: Escherichia coli (E. coli) / References: UniProt: O94913, UniProt: P43364
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: The well solution contained 0.2 M Na acetate, 0.1 M Bis Tris propane pH 7.5 and 20% (w/v) PEG 3350. The drop contained a 1:1 volume ratio of well solution to protein (15 mg/ml in 50 mM Tris, ...Details: The well solution contained 0.2 M Na acetate, 0.1 M Bis Tris propane pH 7.5 and 20% (w/v) PEG 3350. The drop contained a 1:1 volume ratio of well solution to protein (15 mg/ml in 50 mM Tris, pH 7.4, 200 mM NaCl and 5 mM DTT).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→38.79 Å / Num. obs: 56569 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / CC1/2: 0.952 / Rsym value: 0.12 / Net I/σ(I): 19.9
Reflection shellResolution: 2.19→2.25 Å / Num. unique obs: 2745 / CC1/2: 0.757 / Rsym value: 0.372

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHASERphasing
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V0P

4v0p


Resolution: 2.19→38.79 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.162 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.254 / ESU R Free: 0.206
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 2846 5 %RANDOM
Rwork0.2048 ---
obs0.2069 53723 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.55 Å2 / Biso mean: 36.814 Å2 / Biso min: 21.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0.57 Å2-0.25 Å2
2---0.35 Å21.01 Å2
3---0.48 Å2
Refinement stepCycle: final / Resolution: 2.19→38.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7095 0 0 208 7303
Biso mean---45.27 -
Num. residues----882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137258
X-RAY DIFFRACTIONr_bond_other_d0.0030.0176802
X-RAY DIFFRACTIONr_angle_refined_deg1.481.6369831
X-RAY DIFFRACTIONr_angle_other_deg1.4431.56915735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3375869
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9122.5368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.851151256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6011538
X-RAY DIFFRACTIONr_chiral_restr0.0710.2913
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027953
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021529
LS refinement shellResolution: 2.194→2.251 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 156 -
Rwork0.25 3009 -
all-3165 -
obs--71.57 %

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