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- PDB-5wy5: Crystal structure of MAGEG1 and NSE1 complex -

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Basic information

Entry
Database: PDB / ID: 5wy5
TitleCrystal structure of MAGEG1 and NSE1 complex
Components
  • Melanoma-associated antigen G1
  • Non-structural maintenance of chromosomes element 1 homolog
KeywordsMETAL BINDING PROTEIN / E3 LIGASE / ZN
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 / DNA repair / intracellular membrane-bounded organelle / 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 / SAD / Resolution: 2.92 Å
AuthorsYang, M. / Gao, J.
Funding support China, United States, 3items
OrganizationGrant numberCountry
Tsinghua University Startup FundsM.Y. China
National Natural Science Foundation of ChinaSpecial Fund 2060204 China
Sara and Frank McKnight FellowshipP.R.P. United States
CitationJournal: Mol.Cell / Year: 2010
Title: Mage-Ring Protein Complexes Comprise A Family Of E3 Ubiquitin Ligases.
Authors: Doyle, J.M. / Gao, J. / Wang, J. / Yang, M. / Potts, P.R.
History
DepositionJan 11, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 3, 2017ID: 3NW0
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Mar 20, 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
B: Melanoma-associated antigen G1
A: Non-structural maintenance of chromosomes element 1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2956
Polymers53,1152
Non-polymers1794
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-14 kcal/mol
Surface area24120 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
Components on special symmetry positions
IDModelComponents
11B-301-

MG

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Components

#1: Protein Melanoma-associated antigen G1 / Non-SMC element 3 homolog / Hepatocellular carcinoma-associated protein 4 / MAGE-G1 antigen / Non- ...Non-SMC element 3 homolog / Hepatocellular carcinoma-associated protein 4 / MAGE-G1 antigen / Non-structural maintenance of chromosomes element 3 homolog


Mass: 25519.578 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 78-294 / Mutation: I193L, T258L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSMCE3, HCA4, MAGEG1, NDNL2 / Plasmid: PRSFDUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / 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 / Fragment: UNP RESIDUES 9-246 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSMCE1, HSPC333, HSPC337 / Plasmid: PRSFDUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8WV22, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.25 Å3/Da / Density % sol: 62.14 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 5.5
Details: 22%(V/V) PEG 500, 0.1M SODIUM CITRATR PH5.5, 2%(V/V) 1,1,1,3,3,3-HEXAFLUORO-2-PROPANOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBSRF 1W2B10.979
SYNCHROTRONSPring-8 BL38B121
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDJan 15, 2009
RIGAKU RAXIS V2IMAGE PLATEJan 29, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
211
ReflectionResolution: 2.75→40 Å / Num. obs: 17756 / % possible obs: 95.8 % / Observed criterion σ(I): 27.95
Reflection shellResolution: 2.75→2.85 Å / % possible all: 66

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: SAD / Resolution: 2.92→32.36 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.27 707 4.97 %
Rwork0.216 --
obs0.219 14235 91.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.53 Å2 / ksol: 0.28 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.2572 Å2-0 Å2-0 Å2
2---2.4046 Å20 Å2
3----14.0767 Å2
Refinement stepCycle: LAST / Resolution: 2.92→32.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3462 0 4 17 3483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083554
X-RAY DIFFRACTIONf_angle_d1.3264787
X-RAY DIFFRACTIONf_dihedral_angle_d20.7491335
X-RAY DIFFRACTIONf_chiral_restr0.081536
X-RAY DIFFRACTIONf_plane_restr0.008609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9226-3.14810.37391120.34222025X-RAY DIFFRACTION70
3.1481-3.46460.35111470.28042694X-RAY DIFFRACTION93
3.4646-3.96510.29261590.21592831X-RAY DIFFRACTION96
3.9651-4.99270.20811440.17042892X-RAY DIFFRACTION97
4.9927-32.36220.26091450.21183086X-RAY DIFFRACTION98
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)
18.3464-1.0144-3.09240.24611.24873.34061.0559-0.5662.07330.3078-0.6483-0.3942-0.85570.1759-0.20510.5263-0.1529-0.15470.2915-0.00780.6502-0.3027-14.849122.5704
22.3783-1.6904-1.3851.46331.39132.8038-0.3952-0.1361-0.42150.42550.12160.06030.80680.44960.17790.4873-0.15190.02570.4092-0.01950.3712-3.5628-27.573120.2103
32.229-0.0972.7572.0575-1.8412.04530.1460.6925-1.03390.65410.84831.17660.11362.1827-0.17191.20470.1304-0.11530.77890.10450.9396-14.2395-31.375411.515
47.7867-1.76424.82973.3188-0.74189.5309-0.08040.52160.059-0.4488-0.3336-0.120.6352-0.10620.34360.2065-0.0957-0.00380.1596-0.04950.2652-5.4901-35.39661.8117
58.8961-4.77833.68893.0707-1.66052.93930.32150.5109-0.3236-0.7391-0.56760.0160.86550.74990.16580.71130.31690.01510.39210.06650.394814.5211-45.845915.5532
62.6742-0.6195-0.3654.1713-0.44854.0399-0.14610.14430.7893-0.11070.42760.6336-0.1327-0.9271-0.27980.3546-0.1318-0.04920.58030.12260.6825-23.7799-18.167315.7036
77.62890.8926-2.88045.75181.39182.4693-1.422.1166-0.3339-0.79530.986-0.63720.4494-0.58640.31360.5495-0.54480.10320.8312-0.19950.356312.9985-1.1102-3.1439
82.19260.1809-1.97780.57781.72093.2772-0.0223-1.2498-3.64712.5782-1.7239-1.16743.2939-0.78580.88731.8706-0.2436-0.53760.63780.34552.83278.0461-18.33650.7227
9-2.56571.8957-1.81172.6220.69422.817-0.56610.0589-2.07990.73221.45090.45881.02720.125-0.84731.2892-0.20970.66371.1110.31522.542117.7447-16.38994.9383
104.3127-0.50272.1362.4576-2.86820.96-1.5401-1.2868-0.15530.2496-1.74390.76010.7552-0.51051.86071.49130.19450.60832.0074-0.18792.008722.8119-11.241314.5888
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 9:59)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 60:89)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 90:97)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 98:200)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 201:246)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 78:158)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 159:272)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 273:278)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 279:288)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 289:294)

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