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- PDB-9bd3: Structure of the MAGEA4 MHD-RAD18 R6BD Complex -

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Basic information

Entry
Database: PDB / ID: 9bd3
TitleStructure of the MAGEA4 MHD-RAD18 R6BD Complex
Components
  • E3 ubiquitin-protein ligase RAD18
  • Melanoma antigen A 4
KeywordsCELL CYCLE / Rad18 / MAGEA4 / TLS / E3
Function / homology
Function and homology information


Rad6-Rad18 complex / positive regulation of chromosome segregation / Y-form DNA binding / nuclear inclusion body / postreplication repair / protein monoubiquitination / polyubiquitin modification-dependent protein binding / protein autoubiquitination / replication fork / Recognition of DNA damage by PCNA-containing replication complex ...Rad6-Rad18 complex / positive regulation of chromosome segregation / Y-form DNA binding / nuclear inclusion body / postreplication repair / protein monoubiquitination / polyubiquitin modification-dependent protein binding / protein autoubiquitination / replication fork / Recognition of DNA damage by PCNA-containing replication complex / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / single-stranded DNA binding / damaged DNA binding / nuclear body / DNA repair / centrosome / ubiquitin protein ligase binding / DNA damage response / protein-containing complex binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Melanoma-associated antigen 4/5P / E3 ubiquitin-protein ligase Rad18 / 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 ...Melanoma-associated antigen 4/5P / E3 ubiquitin-protein ligase Rad18 / 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 / Rad18-like CCHC zinc finger / Zinc finger, C3HC4 type (RING finger) / SAP domain superfamily / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Melanoma antigen A 4 / E3 ubiquitin-protein ligase RAD18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsForker, K. / Zhou, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Embo J. / Year: 2024
Title: Crystal structure of MAGEA4 MHD-RAD18 R6BD reveals a flipped binding mode compared to AlphaFold2 prediction.
Authors: Forker, K. / Fleming, M.C. / Pearce, K.H. / Vaziri, C. / Bowers, A.A. / Zhou, P.
History
DepositionApr 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 24, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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: E3 ubiquitin-protein ligase RAD18
C: Melanoma antigen A 4
D: E3 ubiquitin-protein ligase RAD18


Theoretical massNumber of molelcules
Total (without water)56,7074
Polymers56,7074
Non-polymers00
Water1,47782
1
A: Melanoma antigen A 4
B: E3 ubiquitin-protein ligase RAD18


Theoretical massNumber of molelcules
Total (without water)28,3532
Polymers28,3532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-17 kcal/mol
Surface area11880 Å2
MethodPISA
2
C: Melanoma antigen A 4
D: E3 ubiquitin-protein ligase RAD18


Theoretical massNumber of molelcules
Total (without water)28,3532
Polymers28,3532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-19 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.210, 85.210, 206.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAGEA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1RN33
#2: Protein/peptide E3 ubiquitin-protein ligase RAD18 / Postreplication repair protein RAD18 / hHR18 / hRAD18 / RING finger protein 73 / RING-type E3 ...Postreplication repair protein RAD18 / hHR18 / hRAD18 / RING finger protein 73 / RING-type E3 ubiquitin transferase RAD18


Mass: 3355.955 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9NS91, RING-type E3 ubiquitin transferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.81 Å3/Da / Density % sol: 67.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% (w/v) PEG 8000 100 mM HEPES/ Sodium hydroxide, pH 7.5, 200 mM Ammonium sulfate, 10% (v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.58→42.6 Å / Num. obs: 26114 / % possible obs: 98.23 % / Redundancy: 6.1 % / Biso Wilson estimate: 53.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0654 / Rpim(I) all: 0.0284 / Net I/σ(I): 19.04
Reflection shellResolution: 2.58→2.672 Å / Rmerge(I) obs: 0.8175 / Mean I/σ(I) obs: 3.79 / Num. unique obs: 2606 / CC1/2: 0.877 / Rpim(I) all: 0.3607

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→42.6 Å / SU ML: 0.3733 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 25.4442
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2255 1305 5 %
Rwork0.1912 24780 -
obs0.1929 26085 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.65 Å2
Refinement stepCycle: LAST / Resolution: 2.58→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3643 0 0 82 3725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313746
X-RAY DIFFRACTIONf_angle_d0.57065067
X-RAY DIFFRACTIONf_chiral_restr0.0399568
X-RAY DIFFRACTIONf_plane_restr0.0054645
X-RAY DIFFRACTIONf_dihedral_angle_d3.9102514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.680.3531440.30872734X-RAY DIFFRACTION98.56
2.68-2.810.32671450.24342752X-RAY DIFFRACTION98.71
2.81-2.950.25821460.23282777X-RAY DIFFRACTION98.62
2.95-3.140.31591460.2462778X-RAY DIFFRACTION98.92
3.14-3.380.24581450.1982746X-RAY DIFFRACTION98.43
3.38-3.720.24121440.18562736X-RAY DIFFRACTION97.56
3.72-4.260.19671450.16442763X-RAY DIFFRACTION98.41
4.26-5.360.17861450.15962753X-RAY DIFFRACTION98.2
5.36-42.60.19921450.18522741X-RAY DIFFRACTION96.81
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)
15.398276337761.108211176932.637585450591.522861529760.3122085598222.914608017960.109921728676-0.165339581560.09944326691830.234605518974-0.169897109149-0.148151380497-0.0501377917550.194682209870.05301574851650.447272679631-0.0280155199295-0.03860708779810.354694912450.03289722105530.422463422339-23.979890607326.3972657633-4.07971354278
22.820063277770.190651492588-0.2821969296393.80267805398-1.070914736833.88291798673-0.03973906429630.143228733275-0.343434183182-0.2434592330120.03173746801520.3508264539250.637819485289-0.357049251770.03777851255160.465066687671-0.0457566838528-0.07582455610810.335812192514-0.004778064103720.390028905522-42.50814466528.02134582958-12.447087876
34.265672766210.2004805883474.876071777175.175458103391.644988609686.19596565076-0.106666380523-0.158386829940.289998416573-0.358152030505-0.0727837066725-0.239119906874-0.1218937049690.908838155118-0.1421382318040.4409251085350.08718460716560.01506305991820.400435621710.01030839234910.40660905639-25.31361564438.78517762885-16.5532755411
44.513672314972.730788528362.653868072427.199448986965.102517210913.784287249920.8477376451720.276844272481-1.306307578160.332734297450.449548109139-1.150982292821.272797679340.521774267267-1.003549577110.7317855782680.0522984544211-0.2421910897080.609178291248-0.02312560207820.76626964231-10.322473268117.99691545142.84242107044
57.184282925390.432967193392-0.6265201700599.291765467192.171587136372.250902635050.11013388747-0.4454310266220.3978694173511.60770475997-0.246101227716-0.5582296456050.7483082208630.9059678825320.03222004641860.611104772787-0.00416205387154-0.1446775638690.4602181562150.06521224988950.484222808828-28.632318951910.4604805613-0.862064660267
64.314937467332.05742276814-2.333797001872.88313788607-1.771021095383.7255364448-0.08398343097380.4975491804760.117066041576-0.01086350104920.00436524977542-0.213262252279-0.093834559370.1201511760110.03314817075050.3684462385130.0736671777990.01901778777750.5587235771260.0769073416110.43259525255-31.59009862140.0265049271-29.8359920541
75.8969884855-1.681162779460.5746280537372.42329423223-0.7213283508454.374126864650.008155607526810.258179750102-0.296094464355-0.0123468631232-0.03291761883760.408061521709-0.020092249862-0.8620254940860.01466138633550.3830959764950.01700719672720.004695088606050.538959938079-0.01729299922560.40086855096-58.034993683435.454125302-22.6034491989
87.567034220693.84681924444-6.367588664896.8666759256-3.549777758589.192778491350.0462288501102-0.1052452688810.9354087719960.1607663835020.2527061922810.103491491564-0.2611072390350.137993556064-0.1662604475620.434702756270.1400131932430.06703032703480.398340804550.01575090355240.492393062854-46.790296137847.3820904234-16.105066968
96.92669497371-1.29414326041-5.879526188821.000025447681.940844975327.164570414541.4861562734-0.520291608692.00143827827-0.5449769574260.1626518540020.250809067234-0.7029272054870.568011761328-1.183915443470.9626435517290.1266559812930.2744460735190.5848788385540.1012148745080.744585948739-30.178760870956.2137974754-34.9238327951
102.956451292-0.937771864006-4.635532179745.32413044163.102165731648.027290316120.108924168171.136254309870.0687782126499-0.359645719066-0.423971479358-0.155242932654-1.11634177971-0.513517954134-0.03417043257870.4116273503180.0780998477715-0.012320003790.7584387059690.18030464180.58997720573-47.422662432946.4270818173-32.27047494
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 100 through 199 )AA100 - 1991 - 100
22chain 'A' and (resid 200 through 283 )AA200 - 283101 - 184
33chain 'A' and (resid 284 through 296 )AA284 - 296185 - 197
44chain 'A' and (resid 297 through 312 )AA297 - 312198 - 213
55chain 'B' and (resid 347 through 366 )BB347 - 3661 - 20
66chain 'C' and (resid 101 through 199 )CC101 - 1991 - 96
77chain 'C' and (resid 200 through 283 )CC200 - 28397 - 180
88chain 'C' and (resid 284 through 296 )CC284 - 296181 - 193
99chain 'C' and (resid 297 through 312 )CC297 - 312194 - 209
1010chain 'D' and (resid 347 through 366 )DD347 - 3661 - 20

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