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- PDB-4v0p: Crystal structure of the MAGE homology domain of human MAGE-A3 -

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Basic information

Entry
Database: PDB / ID: 4v0p
TitleCrystal structure of the MAGE homology domain of human MAGE-A3
ComponentsMELANOMA-ASSOCIATED ANTIGEN 3
KeywordsIMMUNE SYSTEM / MELANOMA ASSOCIATED ANTIGEN / MAGE
Function / homology
Function and homology information


caspase binding / negative regulation of protein processing / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of autophagy / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / histone deacetylase binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / nucleus
Similarity search - Function
MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / 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, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / 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 / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Melanoma-associated antigen 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsNewman, J.A. / Aitkenhead, H. / Cooper, C.D.O. / Pinkas, D.M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
CitationJournal: Plos One / Year: 2016
Title: Structures of Two Melanoma-Associated Antigens Suggest Allosteric Regulation of Effector Binding.
Authors: Newman, J.A. / Cooper, C.D.O. / Roos, A.K. / Aitkenhead, H. / Oppermann, U.C.T. / Cho, H.J. / Osman, R. / Gileadi, O.
History
DepositionSep 17, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MELANOMA-ASSOCIATED ANTIGEN 3


Theoretical massNumber of molelcules
Total (without water)24,1201
Polymers24,1201
Non-polymers00
Water1,820101
1
A: MELANOMA-ASSOCIATED ANTIGEN 3

A: MELANOMA-ASSOCIATED ANTIGEN 3


Theoretical massNumber of molelcules
Total (without water)48,2402
Polymers48,2402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area3330 Å2
ΔGint-26 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.473, 61.473, 292.831
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2050-

HOH

21A-2081-

HOH

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Components

#1: Protein MELANOMA-ASSOCIATED ANTIGEN 3 / / ANTIGEN MZ2-D / CANCER/TESTIS ANTIGEN 1.3 / CT1.3 / MAGE-3 ANTIGEN


Mass: 24119.838 Da / Num. of mol.: 1 / Fragment: MAGE HOMOLOGY DOMAIN, RESIDUES 104-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P43357
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST TWO RESIDUES ARE REMAINING AFTER CLEAVAGE OF PURIFICATION TAG

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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: 3.31 Å3/Da / Density % sol: 62.85 % / Description: NONE
Crystal growDetails: 0.1M MG FORMATE, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.07→53.2 Å / Num. obs: 21270 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 43.24 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.9
Reflection shellResolution: 2.07→2.13 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WA0

2wa0


Resolution: 2.07→39.394 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 24.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 1013 4.8 %
Rwork0.2002 --
obs0.202 21153 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.01 Å2
Refinement stepCycle: LAST / Resolution: 2.07→39.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1663 0 0 101 1764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031708
X-RAY DIFFRACTIONf_angle_d0.7612320
X-RAY DIFFRACTIONf_dihedral_angle_d11.896622
X-RAY DIFFRACTIONf_chiral_restr0.028257
X-RAY DIFFRACTIONf_plane_restr0.003293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.17920.2891480.2742783X-RAY DIFFRACTION100
2.1792-2.31570.36181430.32952777X-RAY DIFFRACTION100
2.3157-2.49450.25331320.23632812X-RAY DIFFRACTION100
2.4945-2.74540.29611330.23252842X-RAY DIFFRACTION100
2.7454-3.14260.25131500.21942861X-RAY DIFFRACTION100
3.1426-3.95870.23921640.19182899X-RAY DIFFRACTION100
3.9587-39.40110.19411430.16483166X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.0147-1.6874-2.12983.69611.87773.32280.08440.01960.2346-0.15890.1814-0.3691-0.32570.4076-0.19780.3260.01330.00270.4421-0.18580.3681-30.934832.24.4517
22.787-0.5459-1.74542.65352.06534.9033-0.1407-0.0808-0.41320.37490.05060.07730.30.29080.10850.3320.0949-0.00240.2993-0.04820.409-44.086833.038723.8888
32.6696-2.53910.30830.94920.163-0.461-0.04370.0252-0.4080.22430.02590.3682-0.17020.14370.0360.62690.02510.12720.39990.00160.7033-36.030918.775927.4989
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 102 THROUGH 162 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 163 THROUGH 268 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 269 THROUGH 310 )

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