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- PDB-7uoa: MAGEA4-MTP1 linear peptide complex -

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Basic information

Entry
Database: PDB / ID: 7uoa
TitleMAGEA4-MTP1 linear peptide complex
Components
  • MTP-1
  • Melanoma antigen A 4
KeywordsPROTEIN BINDING / Mage homology domain MHD
Function / homology
Function and homology information


Melanoma-associated antigen 4/5P / 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
Similarity search - Domain/homology
Melanoma antigen A 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsWilliams, R.S. / Tumbale, P.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1Z01ES102765 United States
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery and Structural Basis of the Selectivity of Potent Cyclic Peptide Inhibitors of MAGE-A4.
Authors: Fleming, M.C. / Chiou, L.F. / Tumbale, P.P. / Droby, G.N. / Lim, J. / Norris-Drouin, J.L. / Williams, J.G. / Pearce, K.H. / Williams, R.S. / Vaziri, C. / Bowers, A.A.
History
DepositionApr 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Melanoma antigen A 4
B: MTP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5434
Polymers26,3592
Non-polymers1842
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-3 kcal/mol
Surface area11090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.387, 79.387, 215.003
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Melanoma antigen A 4 / cDNA / FLJ94494 / Homo sapiens melanoma antigen / family A / 4 (MAGEA4) / mRNA


Mass: 24997.490 Da / Num. of mol.: 1 / Fragment: UNP residues 101-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAGEA4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1RN33
#2: Protein/peptide MTP-1


Mass: 1361.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
Has ligand of interestN

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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: 3.71 Å3/Da / Density % sol: 66.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tris-HCl, magnesium chloride, ethanol

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 5488 / % possible obs: 98.24 % / Redundancy: 10.5 % / CC1/2: 0.992 / Net I/σ(I): 8.65
Reflection shellResolution: 3.5→3.626 Å / Num. unique obs: 5248 / CC1/2: 0.967

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2WA0

2wa0


Resolution: 3.5→49.61 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 32.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2718 924 9.81 %
Rwork0.2472 8495 -
obs0.2496 5469 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.22 Å2 / Biso mean: 116.098 Å2 / Biso min: 70.69 Å2
Refinement stepCycle: final / Resolution: 3.5→49.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 12 0 1662
Biso mean--121.27 --
Num. residues----210
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.690.36041320.33331220135298
3.69-3.920.30041320.2771228136099
3.92-4.220.31071280.25411214134299
4.22-4.640.23611340.2331200133497
4.64-5.310.26921390.2461207134698
5.32-6.690.31231300.26621219134999
6.7-49.610.22411290.2121207133698
Refinement TLS params.Method: refined / Origin x: -28.3398 Å / Origin y: 14.4404 Å / Origin z: -8.0221 Å
111213212223313233
T1.188 Å20.2735 Å2-0.2229 Å2-0.811 Å2-0.029 Å2--0.6308 Å2
L3.1321 °22.1537 °21.8133 °2-4.2593 °22.3571 °2--6.0603 °2
S-0.4082 Å °-0.289 Å °0.2673 Å °-0.403 Å °-0.3367 Å °0.2302 Å °-0.5871 Å °-0.425 Å °0.7758 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA100 - 312
2X-RAY DIFFRACTION1allB1 - 7
3X-RAY DIFFRACTION1allS1 - 2

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