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- PDB-7lgc: MOAP1 CA-like C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 7lgc
TitleMOAP1 CA-like C-terminal domain
ComponentsModulator of apoptosis 1
KeywordsAPOPTOSIS / domesticated Gag
Function / homology
Function and homology information


: / positive regulation of release of cytochrome c from mitochondria / extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway in absence of ligand / apoptotic signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / ubiquitin protein ligase binding ...: / positive regulation of release of cytochrome c from mitochondria / extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway in absence of ligand / apoptotic signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / ubiquitin protein ligase binding / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Paraneoplastic antigen Ma / PNMA
Similarity search - Domain/homology
Modulator of apoptosis 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsZurowska, K. / Pornillos, O. / Ganser-Pornillos, B.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI129678 United States
CitationJournal: Proteins / Year: 2022
Title: Structural evidence that MOAP1 and PEG10 are derived from retrovirus/retrotransposon Gag proteins.
Authors: Zurowska, K. / Alam, A. / Ganser-Pornillos, B.K. / Pornillos, O.
History
DepositionJan 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Modulator of apoptosis 1
B: Modulator of apoptosis 1


Theoretical massNumber of molelcules
Total (without water)24,8542
Polymers24,8542
Non-polymers00
Water3,099172
1
A: Modulator of apoptosis 1


Theoretical massNumber of molelcules
Total (without water)12,4271
Polymers12,4271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Modulator of apoptosis 1


Theoretical massNumber of molelcules
Total (without water)12,4271
Polymers12,4271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.034, 34.126, 57.673
Angle α, β, γ (deg.)97.734, 93.907, 94.640
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 247 or (resid 248 through 249...
d_2ens_1(chain "B" and (resid 247 through 307 or resid 309 through 347))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROILEA3 - 63
d_12ens_1ARGGLUA65 - 103
d_21ens_1PROILEB1 - 61
d_22ens_1ARGGLUB65 - 103

NCS oper: (Code: givenMatrix: (0.0850261478233, -0.996375649977, 0.0024735238471), (-0.99637026138, -0.0850149345878, 0.00433164337043), (-0.00410565751062, -0.0028328485516, -0.999987559195)Vector: ...NCS oper: (Code: given
Matrix: (0.0850261478233, -0.996375649977, 0.0024735238471), (-0.99637026138, -0.0850149345878, 0.00433164337043), (-0.00410565751062, -0.0028328485516, -0.999987559195)
Vector: 6.97412679285, 3.75361519867, 34.6214735806)

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Components

#1: Protein Modulator of apoptosis 1 / MAP1 / Paraneoplastic antigen Ma4


Mass: 12427.097 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MOAP1, PNMA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96BY2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Tris 20% PEG 3350 3% hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 20575 / % possible obs: 94.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 18.77 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.039 / Rrim(I) all: 0.093 / Net I/σ(I): 18.35
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 713 / Rpim(I) all: 0.604 / Rrim(I) all: 1 / % possible all: 65.5

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Low resolution experimental model

Resolution: 1.85→30.16 Å / SU ML: 0.2408 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.6924
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2547 893 4.64 %
Rwork0.207 18371 -
obs0.2092 19264 88.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.91 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 0 172 1764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00581621
X-RAY DIFFRACTIONf_angle_d0.75672200
X-RAY DIFFRACTIONf_chiral_restr0.041263
X-RAY DIFFRACTIONf_plane_restr0.0072287
X-RAY DIFFRACTIONf_dihedral_angle_d18.8439623
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.806472204472 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.970.2995890.25821707X-RAY DIFFRACTION49.37
1.97-2.120.28231640.24183062X-RAY DIFFRACTION88.72
2.12-2.330.25971500.21193363X-RAY DIFFRACTION97.23
2.33-2.670.27611770.21113364X-RAY DIFFRACTION97.76
2.67-3.360.25231700.20713431X-RAY DIFFRACTION98.25
3.36-30.160.22841430.18953444X-RAY DIFFRACTION98.95

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