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- PDB-5hvq: Alternative model of the MAGE-G1 NSE-1 complex -

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Basic information

Entry
Database: PDB / ID: 5hvq
TitleAlternative model of the MAGE-G1 NSE-1 complex
Components
  • Melanoma-associated antigen G1
  • Non-structural maintenance of chromosomes element 1 homolog
KeywordsLIGASE / complex Melanoma antigen RING-containing E3 ligases
Function / homology
Function and homology information


cellular response to radiation / Smc5-Smc6 complex / cellular response to hydroxyurea / chromatin looping / regulation of telomere maintenance / protein sumoylation / SUMOylation of DNA damage response and repair proteins / positive regulation of protein ubiquitination / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase ...cellular response to radiation / Smc5-Smc6 complex / cellular response to hydroxyurea / chromatin looping / regulation of telomere maintenance / protein sumoylation / SUMOylation of DNA damage response and repair proteins / positive regulation of protein ubiquitination / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / cellular response to UV / ubiquitin protein ligase activity / chromosome, telomeric region / protein dimerization activity / intracellular membrane-bounded organelle / DNA repair / DNA damage response / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Aspartate Aminotransferase, domain 1 - #220 / Non-structural maintenance of chromosomes element 1 / Zinc finger, RING-like / Nse1 non-SMC component of SMC5-6 complex / RING-like domain / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif ...Aspartate Aminotransferase, domain 1 - #220 / Non-structural maintenance of chromosomes element 1 / Zinc finger, RING-like / Nse1 non-SMC component of SMC5-6 complex / RING-like domain / 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 / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Aspartate Aminotransferase, domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Arc Repressor Mutant, subunit A / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Non-structural maintenance of chromosomes element 1 homolog / Non-structural maintenance of chromosomes element 3 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.923 Å
AuthorsNewman, J.A. / Cooper, C.D.O. / Roos, A.K. / Aitkenhead, H. / Oppermann, U.C.T. / Cho, H.J. / Osman, R. / 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. / Roos, A.K. / Aitkenhead, H. / Oppermann, U.C. / Cho, H.J. / Osman, R. / Gileadi, O.
History
DepositionJan 28, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Melanoma-associated antigen G1
C: Non-structural maintenance of chromosomes element 1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2464
Polymers53,1152
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-6 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.257, 154.327, 53.726
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Melanoma-associated antigen G1 / Hepatocellular carcinoma-associated protein 4 / MAGE-G1 antigen / Necdin-like protein 2


Mass: 25519.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDNL2, HCA4, MAGEG1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96MG7
#2: Protein Non-structural maintenance of chromosomes element 1 homolog / Non-SMC element 1 homolog


Mass: 27595.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSMCE1, HSPC333, HSPC337 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8WV22, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: As for entry 3nw0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.923→32.36 Å / Num. obs: 14235 / % possible obs: 98 % / Redundancy: 2 % / Net I/σ(I): 10

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Processing

Software
NameVersionClassification
PHENIX1.9_1682refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 2.923→32.36 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2678 756 4.97 %
Rwork0.2367 --
obs0.2383 15209 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.923→32.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3537 0 0 0 3537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033607
X-RAY DIFFRACTIONf_angle_d0.6854863
X-RAY DIFFRACTIONf_dihedral_angle_d14.0081380
X-RAY DIFFRACTIONf_chiral_restr0.026539
X-RAY DIFFRACTIONf_plane_restr0.003621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9226-3.14810.42821410.38862579X-RAY DIFFRACTION89
3.1481-3.46460.34041580.30412892X-RAY DIFFRACTION100
3.4646-3.96510.29871660.25192922X-RAY DIFFRACTION99
3.9651-4.99270.22551450.20912947X-RAY DIFFRACTION99
4.9927-32.36220.23561460.21343113X-RAY DIFFRACTION99
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)
15.3692-1.4272-0.04235.65212.05338.48460.13370.4591-0.7687-0.2620.3838-0.6417-0.1951.0934-0.41760.3728-0.09630.04730.6267-0.07960.612823.139317.637315.7243
23.31751.677-2.05023.53183.24818.4961-0.1721-0.04631.14551.55271.27451.28280.3519-0.12-1.29891.5425-0.02690.07631.71510.21931.12163.9778-0.91647.6873
36.4023.5430.16064.48522.54713.1506-1.73781.96231.7826-1.35191.28471.0038-1.024-0.91880.32761.1089-0.6498-0.12141.24650.20180.5133-11.02912.3214-2.644
42.00815.5543-2.06283.8715-0.52690.8541-0.75413.08221.8634-2.11440.95120.7245-0.5204-0.3486-0.50561.3533-0.39910.19742.09280.23110.7713-13.1392.8753-12.8322
57.2097-1.67413.0842.7568-0.28861.39670.99970.1967-3.603-2.40311.45280.3256-0.69430.0873-2.251.7844-0.8726-0.09581.81220.10261.4726-15.9528-8.4953-7.5068
69.1477-1.3405-0.33418.2147-0.72713.6885-0.95010.3331.4145-0.28920.80021.1774-0.60460.34080.20510.795-0.2092-0.21210.86750.12691.0064-16.73227.05711.5472
78.22191.20012.16056.771-0.71256.0920.2794-0.4487-1.72350.6929-0.1520.61340.7748-0.4128-0.22710.692-0.15820.12240.65620.01670.91871.7815.872623.1592
81.6568-2.43420.92064.77030.32974.17650.79380.04930.4291-0.3302-0.3573-0.6078-0.220.3031-0.42370.5945-0.09080.08620.50270.03370.54485.568229.147114.6434
99.5836-3.7832-5.99452.68873.09427.15520.46250.79380.3528-0.5071-0.3991-0.1082-0.9494-0.6058-0.05120.6095-0.0182-0.03550.44940.05550.448-1.096739.10096.1484
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 78 through 161 )
2X-RAY DIFFRACTION2chain 'D' and (resid 162 through 173 )
3X-RAY DIFFRACTION3chain 'D' and (resid 174 through 188 )
4X-RAY DIFFRACTION4chain 'D' and (resid 189 through 219 )
5X-RAY DIFFRACTION5chain 'D' and (resid 220 through 229 )
6X-RAY DIFFRACTION6chain 'D' and (resid 230 through 294 )
7X-RAY DIFFRACTION7chain 'C' and (resid 9 through 67 )
8X-RAY DIFFRACTION8chain 'C' and (resid 68 through 102 )
9X-RAY DIFFRACTION9chain 'C' and (resid 103 through 246 )

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