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- PDB-9bd2: MAGE-A3 MHD crystal soaked with KL861 -

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Basic information

Entry
Database: PDB / ID: 9bd2
TitleMAGE-A3 MHD crystal soaked with KL861
ComponentsMelanoma-associated antigen 3
KeywordsONCOPROTEIN / MAGE-A3 / Melanoma-associated antigen 3 / MAGE / MAGE-A3 MHD / KL861
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 / histone deacetylase binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / nucleus
Similarity search - Function
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-associated antigen 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsButrin, A. / Krone, M.W. / Li, K. / Bond, M.J. / Linhares, B.M. / Crews, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Development of Ligands and Degraders Targeting MAGE-A3.
Authors: Li, K. / Krone, M.W. / Butrin, A. / Bond, M.J. / Linhares, B.M. / Crews, C.M.
History
DepositionApr 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 25, 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-associated antigen 3
B: Melanoma-associated antigen 3
C: Melanoma-associated antigen 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5564
Polymers71,0263
Non-polymers5301
Water1,20767
1
A: Melanoma-associated antigen 3

A: Melanoma-associated antigen 3


Theoretical massNumber of molelcules
Total (without water)47,3512
Polymers47,3512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2860 Å2
ΔGint-16 kcal/mol
Surface area22830 Å2
MethodPISA
2
B: Melanoma-associated antigen 3
C: Melanoma-associated antigen 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8813
Polymers47,3512
Non-polymers5301
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-13 kcal/mol
Surface area22650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.659, 103.402, 325.668
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-332-

HOH

21A-334-

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: 23675.445 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAGEA3, MAGE3 / Production host: Escherichia coli (E. coli) / References: UniProt: P43357
#2: Chemical ChemComp-A1AL3 / (furan-2-yl)[4-({(5P)-5-(1H-indazol-4-yl)-2-[3-(morpholin-4-yl)propoxy]phenyl}methyl)piperazin-1-yl]methanone


Mass: 529.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H35N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.3 Å3/Da / Density % sol: 62.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: MAGE-A3 MHD was buffer-exchanged into 25 mM HEPES, 150 mM NaCl, pH 7.5 buffer using 10 kDa MWCO Centricon and concentrated to 5 mg/mL. MAGE-A3 MHD was crystallized using the hanging drop ...Details: MAGE-A3 MHD was buffer-exchanged into 25 mM HEPES, 150 mM NaCl, pH 7.5 buffer using 10 kDa MWCO Centricon and concentrated to 5 mg/mL. MAGE-A3 MHD was crystallized using the hanging drop vapor diffusion method in 16% PEG8000, 40 mM potassium phosphate, 20% glycerol. For each hanging drop, 2 ul of protein solution was mixed with an equal volume of well solution and incubated at 4 C. Once the crystals reached their maximum size, they were transferred to a cryo-protectant solution (well solution containing 30% glycerol and 1 mM KL861) and soaked with KL861 for 3.5 hours. The soaked crystals were flash-frozen in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.23→81.42 Å / Num. obs: 46101 / % possible obs: 99.9 % / Redundancy: 8.9 % / Biso Wilson estimate: 53.05 Å2 / CC1/2: 0.99 / Net I/σ(I): 11.4
Reflection shellResolution: 2.23→2.27 Å / Num. unique obs: 2251 / CC1/2: 0.321

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→81.42 Å / SU ML: 0.3531 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.2304
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2602 2335 5.07 %
Rwork0.2181 43745 -
obs0.2202 46080 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.2 Å2
Refinement stepCycle: LAST / Resolution: 2.24→81.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4960 0 39 67 5066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00365131
X-RAY DIFFRACTIONf_angle_d0.71676964
X-RAY DIFFRACTIONf_chiral_restr0.0433772
X-RAY DIFFRACTIONf_plane_restr0.0059882
X-RAY DIFFRACTIONf_dihedral_angle_d7.7427694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.280.39071130.33692535X-RAY DIFFRACTION99.66
2.28-2.330.34411430.32062546X-RAY DIFFRACTION99.89
2.33-2.390.35411300.29342510X-RAY DIFFRACTION100
2.39-2.440.38121320.28522584X-RAY DIFFRACTION99.89
2.44-2.510.30071180.29392533X-RAY DIFFRACTION99.96
2.51-2.580.35961130.30492590X-RAY DIFFRACTION99.96
2.58-2.670.34131420.28582557X-RAY DIFFRACTION99.93
2.67-2.760.3491570.25632499X-RAY DIFFRACTION99.89
2.76-2.870.28171430.24682539X-RAY DIFFRACTION99.89
2.87-3.010.28081540.22842519X-RAY DIFFRACTION100
3.01-3.160.25521700.23962558X-RAY DIFFRACTION100
3.16-3.360.28541160.24962597X-RAY DIFFRACTION99.96
3.36-3.620.27351410.21262580X-RAY DIFFRACTION99.82
3.62-3.990.25831570.20562580X-RAY DIFFRACTION99.71
3.99-4.560.24221310.18042599X-RAY DIFFRACTION100
4.56-5.750.22371400.19112647X-RAY DIFFRACTION99.96
5.75-81.420.2021350.1872772X-RAY DIFFRACTION99.83
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)
12.935114769740.3956015559840.3085883305374.61098943752-0.2199475524761.729903622960.4108033963930.258682245884-0.46324091459-0.8260477097210.317985057673-0.5898634891110.8024848518590.0343638177508-0.6225063818410.784252775177-0.11551940226-0.1555650248280.478036283370.01098150539540.541704665061-12.955948374810.320259741559.3836928744
22.253028556820.3576262716860.8976211402270.696237137696-0.0736873337310.7131118470830.01381241726720.02026574095690.131890264773-0.5330180792430.3181099055650.3314801946820.5045004813780.0209287778934-0.2383012603240.64253977968-0.136911764689-0.1292997240160.5323723700110.116509961360.487054490502-19.4057677816.204172703960.5113727251
33.46702399185-0.2782481139780.5782286441911.697574021920.3841445376661.92699300648-0.0340791422402-0.3477324818040.218318642890.1163198416270.07686931679040.07381160023950.0629223904248-0.267217773844-0.04283355819660.288647553417-0.0281021971047-0.0213404377240.4960072487250.02874084251720.438259405556-10.974321237422.80273812484.3323297423
41.55746187697-1.772948497791.332573161535.579189400921.196648599574.73522795669-1.00338230613-0.3731724498230.2833183018151.24115282244-0.0402721758218-0.7915193095190.9978292618940.5726718813460.3049414289670.478202207601-0.08367541283360.01521584311770.638234063023-0.1592446243110.656990606617-40.86414729227.9496722763789.0288968802
56.07706931935-0.6114289374931.147046538712.29594117619-0.2270663026252.576860720220.250116548205-0.388546489976-0.345663993671-0.0946099200002-0.06665024288280.3239130211450.262492798723-0.339818085935-0.008355716379290.5755949595610.03635709234260.03399317887880.5680185563490.05773802531890.531729473146-53.066299490419.03747753518.49219830202
63.789037358581.30717901515-1.330984392484.021800702560.8471277225632.4546349553-0.3479643526430.304034488-0.363462968506-0.5484021981830.0892861782838-0.4403893841940.2720028263340.1561517318610.2568459625340.5872605984960.05991043962370.08726968538790.6691957316930.08662688192850.528675082365-42.868044103121.05181484230.964345989738
71.10731890577-0.01791813841951.010080392160.860544254195-1.542643497270.926355849982-0.15046640889-0.02856495754910.221325283085-0.134112985781-0.106349963247-0.2073987942430.1733395750390.1924220474560.2122762504490.5089344775190.06152354271580.0393646564530.6387699959520.03278503567980.400846628548-42.827260735923.672789832610.6181870145
81.80404608676-0.8795035685770.1571916518113.53586337033-0.8179500628394.25139785697-0.00310200921493-0.2289812797930.08409088825330.379501121512-0.318744457613-0.228605676958-0.138158855267-0.637032473340.2524947167710.441505782218-0.0671728667184-0.06008716124840.534459728863-0.00543408688320.454237420115-38.836751797318.822919625935.2619740279
94.603025373262.05326098939-0.8830822352684.242926450041.839524303841.89158814713-0.4449529203970.8007993548480.1961667287220.150525196147-0.118849935659-0.276421642742-0.594386317765-0.08630700921860.2372570257490.8454553975230.17015051753-0.1068788702420.6106199343990.08455573499240.674916386518-41.59884935533.302600739125.3764317816
101.26640812511.38648374707-1.274118103421.50893841393-1.64373571215.07110370346-0.2896795153190.191159166627-0.7276467073110.9220311724310.0118307479191-1.020457634260.67139348951-0.3438275892080.1235721865140.657918170109-0.2174410246970.1090950743280.707813631957-0.0834679056110.855959282785-65.562547378139.025446219834.8051668539
114.334016196242.166882321151.169088370866.02048084485-0.5920930363411.96217645519-0.3641035329260.4490426881960.409239273757-0.1464503632190.5702427970731.225895112260.0390425972576-0.371249064062-0.07965931076580.640204726643-0.131872186767-0.003418553082030.4899487488690.1009208834340.501816874393-42.6179081308-10.004314010447.2333290995
123.057792512311.52819079284-0.4205991895897.08508123981-2.99680529194.92743708433-0.243398588989-0.1315025598770.531764411310.76048245389-0.153401735080.4160769179520.149831143205-0.1716703648780.2322269066881.04258558689-0.208600418096-0.03468084231820.6351802163590.008293586194010.439834358809-36.1204103391-4.749512304856.2827320612
132.160791126471.40148916895-0.009807384845924.31577756491-3.620118416014.422277422930.160968196931-0.150971144905-0.4759344592870.568153677576-0.299253636126-0.304501901838-0.609421593218-0.7632906305950.400631205120.603936472502-0.169193447535-0.00706038035810.4206396115270.003067471097990.424552942865-37.1583860351-14.25785028548.7894687807
141.56964365987-0.3087340476170.5609286165233.74158189009-0.9453815524693.43626537790.116410636760.247611157792-0.145740378392-0.116652664596-0.288753710786-0.6527699159530.3987407401210.1820287499120.1540681512840.504268376612-0.06936481914910.03056448899220.409630444210.05176001230320.581780173356-28.4271396725-1.125813707930.332565038
155.224187945780.367786607177-0.3585686802761.04043660703-1.951991893513.86430005387-0.745791100471-0.07400057915060.0733851038075-0.000878336993107-0.1718694849291.159720114351.35912568675-0.08421691750250.2588429154320.867762994907-0.1735747740620.130745250111.13206587117-0.1530978465540.625702863779-25.6896040513-34.605659259919.1491643755
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 39 )AA1 - 391 - 39
22chain 'A' and (resid 40 through 82 )AA40 - 8240 - 82
33chain 'A' and (resid 83 through 192 )AA83 - 19283 - 192
44chain 'A' and (resid 193 through 209 )AA193 - 209193 - 209
55chain 'B' and (resid 1 through 24 )BB1 - 241 - 24
66chain 'B' and (resid 25 through 39 )BB25 - 3925 - 39
77chain 'B' and (resid 40 through 97 )BB40 - 9740 - 97
88chain 'B' and (resid 98 through 181 )BB98 - 18198 - 181
99chain 'B' and (resid 182 through 193 )BB182 - 193182 - 193
1010chain 'B' and (resid 194 through 209 )BB194 - 209194 - 209
1111chain 'C' and (resid 1 through 24 )CC1 - 241 - 24
1212chain 'C' and (resid 25 through 39 )CC25 - 3925 - 39
1313chain 'C' and (resid 40 through 61 )CC40 - 6140 - 61
1414chain 'C' and (resid 62 through 193 )CC62 - 19362 - 193
1515chain 'C' and (resid 194 through 209 )CC194 - 209194 - 209

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