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- PDB-7aov: Crystal Structure of a TRPM2 Domain -

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Basic information

Entry
Database: PDB / ID: 7aov
TitleCrystal Structure of a TRPM2 Domain
ComponentsTransient receptor potential cation channel subfamily M member 2
KeywordsSIGNALING PROTEIN / TRPM2
Function / homology
Function and homology information


TRP channels / ligand-gated monoatomic cation channel activity / Neutrophil degranulation / ADP-D-ribose binding / mono-ADP-D-ribose binding / ligand-gated calcium channel activity / calcium ion transmembrane transport / calcium channel activity / monoatomic ion channel activity / protein homotetramerization ...TRP channels / ligand-gated monoatomic cation channel activity / Neutrophil degranulation / ADP-D-ribose binding / mono-ADP-D-ribose binding / ligand-gated calcium channel activity / calcium ion transmembrane transport / calcium channel activity / monoatomic ion channel activity / protein homotetramerization / calcium ion binding / plasma membrane
Similarity search - Function
TRPM, SLOG domain / SLOG in TRPM / NUDIX hydrolase-like domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily M member 2
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.00001625778 Å
AuthorsSander, S. / Tidow, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 1328 Germany
CitationJournal: Protein Sci. / Year: 2022
Title: The crystal structure of TRPM2 MHR1/2 domain reveals a conserved Zn 2+ -binding domain essential for structural integrity and channel activity.
Authors: Sander, S. / Pick, J. / Gattkowski, E. / Fliegert, R. / Tidow, H.
History
DepositionOct 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily M member 2
B: Transient receptor potential cation channel subfamily M member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1264
Polymers95,9952
Non-polymers1312
Water7,422412
1
A: Transient receptor potential cation channel subfamily M member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0632
Polymers47,9981
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transient receptor potential cation channel subfamily M member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0632
Polymers47,9981
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.760, 188.128, 47.773
Angle α, β, γ (deg.)90.000, 102.659, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Transient receptor potential cation channel subfamily M member 2


Mass: 47997.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: trpm2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 Gold (DE3) / References: UniProt: A0A0R4IMY7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: Tris, BICINE, Diethylene glycol, Triethylene glycol, Tetraethylene glycol, Pentaethylene glycol, glycerol, PEG4000, Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2→46.62 Å / Num. obs: 53708 / % possible obs: 97.15 % / Redundancy: 13.9 % / Biso Wilson estimate: 34.4560992986 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.28
Reflection shellResolution: 2→2.071 Å / Mean I/σ(I) obs: 1.46 / Num. unique obs: 5374 / CC1/2: 0.552 / % possible all: 96.91

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.00001625778→46.6117154188 Å / SU ML: 0.242429295894 / Cross valid method: FREE R-VALUE / σ(F): 1.34245382405 / Phase error: 25.4548106828
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.231176397768 2739 5.10350481656 %
Rwork0.188124451293 50930 -
obs0.190409700336 53669 97.1472531451 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.5160232049 Å2
Refinement stepCycle: LAST / Resolution: 2.00001625778→46.6117154188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5956 0 2 412 6370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008051751513556074
X-RAY DIFFRACTIONf_angle_d0.9270233389748200
X-RAY DIFFRACTIONf_chiral_restr0.0530808292072920
X-RAY DIFFRACTIONf_plane_restr0.005587475185111040
X-RAY DIFFRACTIONf_dihedral_angle_d6.700739917293638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.00001625778-2.03450.2860628954041490.2532399033292468X-RAY DIFFRACTION97.0697329377
2.0345-2.07150.3305867799851360.263775963472614X-RAY DIFFRACTION96.7969024991
2.0715-2.11130.3158150745221230.2417247077772522X-RAY DIFFRACTION97.4217311234
2.1113-2.15440.3420748703941420.2403544596872501X-RAY DIFFRACTION95.4496208017
2.1544-2.20130.2758691140881310.2189236178142546X-RAY DIFFRACTION97.0982952485
2.2013-2.25250.2933487331731250.2186470488812555X-RAY DIFFRACTION97.7745348413
2.2525-2.30880.2703575680051370.2071631963692548X-RAY DIFFRACTION96.8265416516
2.3088-2.37120.21016772041410.2035971800772506X-RAY DIFFRACTION95.559566787
2.3712-2.4410.2570226692181250.2056592602462497X-RAY DIFFRACTION97.1830985915
2.441-2.51980.3236020958341390.2032349139982624X-RAY DIFFRACTION97.8746014878
2.5198-2.60980.2511270515391190.2040278821722555X-RAY DIFFRACTION98.344979772
2.6098-2.71430.2492042728271640.2133053138882524X-RAY DIFFRACTION97.6034858388
2.7143-2.83780.2551235057531110.2019614739882601X-RAY DIFFRACTION97.2391538186
2.8378-2.98740.2962205367941220.1963113362982598X-RAY DIFFRACTION97.0388869069
2.9874-3.17460.2278897068161570.2060536689562512X-RAY DIFFRACTION98.0889378905
3.1746-3.41960.2509879587311490.1896415991642551X-RAY DIFFRACTION96.9827586207
3.4196-3.76360.2182745622271450.1690536176142532X-RAY DIFFRACTION97.700729927
3.7636-4.30790.1958626245921380.1518256556062584X-RAY DIFFRACTION97.7027997128
4.3079-5.42620.1794243545561750.1520724402692527X-RAY DIFFRACTION97.5451263538
5.4262-46.61171541880.1957035271611110.1875390975032565X-RAY DIFFRACTION95.8109559613
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)
11.558647650830.892113064498-0.506366151244.675734977370.0723450968011.284816352270.226609590047-0.141691501183-0.01852826743460.0979719439314-0.0952831752124-0.587931543378-0.0215403395460.0981927279511-0.1120081017190.3138527507310.0121414655279-0.03328225324750.277526022894-0.01027434432850.28417426697630.2994391963-23.361199169810.0146450054
23.012704326930.7582192615651.213127471061.974009271330.4496349401111.089939300310.127586017747-0.20742472368-0.06848085020950.324630824468-0.0461889476410.02991459721140.0760683108843-0.136352995941-0.07089857522750.2893952492480.003058772591710.0143948075590.2333520027050.02613501728610.144300411.1165938314-34.50363960256.46581070027
31.520431618990.2212990131190.03071040649343.4162045206-0.23528830911.489605773030.08517155537030.1264944076350.108132392639-0.459685524909-0.0388411986174-0.0588081135296-0.01327595876320.0906687981994-0.07172245788750.3545804540590.01721493020310.01345221314290.3542933881230.03809381204660.2212450259753.72211618681-26.2398685906-13.519988096
43.6433166072-1.34602654906-0.2739749251646.3034422382-1.481995124624.84092981478-0.2018310735050.868689640766-0.347564471985-0.8361124384430.01158645033350.7046764406660.244680870588-0.8335633567010.2679040457940.451968840441-0.0338341572933-0.130627973680.401056554128-0.06910150195930.309456319118-3.17047211202-39.4783499158-14.1396953227
51.36779323386-0.0939613032924-0.7377948202495.091325842051.081690193091.51392148277-0.03614984950390.127113216586-0.163075757738-0.575333307774-0.2015465056350.0514208750598-0.115726151648-0.09732625265820.2153628421750.3015040813040.000196092306525-0.04305795518560.3170472236680.002449985190770.29178811454815.5256517572-81.2805758139-8.45012804325
60.6001238338020.2381104252560.737304806712.028098325010.6833709306032.53603703771-0.0970104756704-0.04021756452080.111369604589-0.0808044086828-0.0630232337740.385510458629-0.251827291644-0.3303441564050.1429272322770.2107795189650.0212036231203-0.01134030200120.270665587566-0.008241175618830.29918569079314.1964914364-67.880775565512.2328544918
71.6020592661-0.8254267321410.9686112895652.521937303731.01760570443.13304422322-0.0775131723693-0.12367481522-0.01623960737810.01837842576730.046308648597-0.0883657378073-0.02576530411480.1486530111450.003953304530670.159106634611-0.0174848648771-0.004316782055670.2151424714580.02848228962010.18727297609722.2515938078-72.282072516310.652932118
81.85198809657-0.4403560550080.1211894638494.69455120384-0.5239474172431.61868880182-0.0528084296124-0.113878295869-0.009987867998390.41782149286-0.0176867440224-0.4693755402960.03252740573590.2473969266180.07846787958720.2175175230260.00705405244964-0.05219288214550.2869354929840.002021901737860.24476458489632.6690372519-77.533741028727.4587586438
Refinement TLS group
IDRefine-IDRefine TLS-IDLabel asym-IDLabel seq-ID
1X-RAY DIFFRACTION1A38 - 111
2X-RAY DIFFRACTION2A112 - 292
3X-RAY DIFFRACTION3A293 - 391
4X-RAY DIFFRACTION4A392 - 423
5X-RAY DIFFRACTION5B38 - 111
6X-RAY DIFFRACTION6B112 - 244
7X-RAY DIFFRACTION7B245 - 326
8X-RAY DIFFRACTION8B327 - 423

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