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- PDB-7px2: Conotoxin Mu8.1 from Conus mucronatus -

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Basic information

Entry
Database: PDB / ID: 7px2
TitleConotoxin Mu8.1 from Conus mucronatus
ComponentsConotoxin Mu8.1
KeywordsTOXIN / Conotoxin
Biological speciesConus mucronatus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsMueller, E. / Hackney, C. / Ellgaard, L. / Morth, J.P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
CitationJournal: Plos Biol. / Year: 2023
Title: A previously unrecognized superfamily of macro-conotoxins includes an inhibitor of the sensory neuron calcium channel Cav2.3.
Authors: Hackney, C.M. / Florez Salcedo, P. / Mueller, E. / Koch, T.L. / Kjelgaard, L.D. / Watkins, M. / Zachariassen, L. / Tuelund, P.S. / McArthur, J.R. / Adams, D.J. / Kristensen, A.S. / Olivera, ...Authors: Hackney, C.M. / Florez Salcedo, P. / Mueller, E. / Koch, T.L. / Kjelgaard, L.D. / Watkins, M. / Zachariassen, L. / Tuelund, P.S. / McArthur, J.R. / Adams, D.J. / Kristensen, A.S. / Olivera, B. / Finol-Urdaneta, R.K. / Safavi-Hemami, H. / Morth, J.P. / Ellgaard, L.
History
DepositionOct 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conotoxin Mu8.1
B: Conotoxin Mu8.1
C: Conotoxin Mu8.1
D: Conotoxin Mu8.1
E: Conotoxin Mu8.1
F: Conotoxin Mu8.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,65112
Polymers61,2216
Non-polymers1,4306
Water2,216123
1
A: Conotoxin Mu8.1
B: Conotoxin Mu8.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8844
Polymers20,4072
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Conotoxin Mu8.1
D: Conotoxin Mu8.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8844
Polymers20,4072
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Conotoxin Mu8.1
F: Conotoxin Mu8.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8844
Polymers20,4072
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.840, 88.450, 69.310
Angle α, β, γ (deg.)90.000, 116.710, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 7 through 12 or resid 15...
d_2ens_1(chain "B" and (resid 7 through 12 or resid 15...
d_3ens_1(chain "C" and (resid 7 through 12 or resid 15...
d_4ens_1(chain "D" and (resid 7 through 12 or resid 15...
d_5ens_1(chain "E" and (resid 7 through 12 or resid 15...
d_6ens_1(chain "F" and (resid 7 through 12 or resid 15...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LEULEULEULEUAA7 - 127 - 12
d_12PHEPHETHRTHRAA15 - 3915 - 39
d_13ILEILEGLYGLYAA41 - 6541 - 65
d_14THRTHRASPASPAA67 - 6967 - 69
d_15CYSCYSLEULEUAA71 - 8671 - 86
d_16CYSCYSCYSCYSAA8989
d_17EPEEPEEPEEPEAG101
d_21LEULEULEULEUBB7 - 127 - 12
d_22PHEPHETHRTHRBB15 - 3915 - 39
d_23ILEILEGLYGLYBB41 - 6541 - 65
d_24THRTHRASPASPBB67 - 6967 - 69
d_25CYSCYSLEULEUBB71 - 8671 - 86
d_26CYSCYSCYSCYSBB8989
d_27EPEEPEEPEEPEBH101
d_31LEULEULEULEUCC7 - 127 - 12
d_32PHEPHETHRTHRCC15 - 3915 - 39
d_33ILEILEGLYGLYCC41 - 6541 - 65
d_34THRTHRASPASPCC67 - 6967 - 69
d_35CYSCYSLEULEUCC71 - 8671 - 86
d_36CYSCYSCYSCYSCC8989
d_37EPEEPEEPEEPECI101
d_41LEULEULEULEUDD7 - 127 - 12
d_42PHEPHETHRTHRDD15 - 3915 - 39
d_43ILEILEGLYGLYDD41 - 6541 - 65
d_44THRTHRASPASPDD67 - 6967 - 69
d_45CYSCYSLEULEUDD71 - 8671 - 86
d_46CYSCYSCYSCYSDD8989
d_47EPEEPEEPEEPEDJ101
d_51LEULEULEULEUEE7 - 127 - 12
d_52PHEPHETHRTHREE15 - 3915 - 39
d_53ILEILEGLYGLYEE41 - 6541 - 65
d_54THRTHRASPASPEE67 - 6967 - 69
d_55CYSCYSLEULEUEE71 - 8671 - 86
d_56CYSCYSCYSCYSEE8989
d_57EPEEPEEPEEPEEK101
d_61LEULEULEULEUFF7 - 127 - 12
d_62PHEPHETHRTHRFF15 - 3915 - 39
d_63ILEILEGLYGLYFF41 - 6541 - 65
d_64THRTHRASPASPFF67 - 6967 - 69
d_65CYSCYSLEULEUFF71 - 8671 - 86
d_66CYSCYSCYSCYSFF8989
d_67EPEEPEEPEEPEFL101

NCS oper:
IDCodeMatrixVector
1given(-0.996743146859, -0.0784871620179, 0.0185166030288), (-0.0801202104307, 0.937763730613, -0.337905219593), (0.00915702298232, -0.338288266048, -0.940997979798)-8.75585047283, 10.5620655318, 63.0380582282
2given(0.046502391944, 0.482817734751, -0.874485312943), (0.795658123118, -0.547200264087, -0.259807663667), (-0.603958341825, -0.683709664985, -0.409603973792)19.873532574, 17.0054050864, 17.7215390634
3given(-0.0888918160039, 0.75561998799, 0.648950444023), (-0.765132226027, -0.468938770828, 0.44121322046), (0.637707551894, -0.457312653405, 0.619834022375)-30.2270176869, -12.4366423272, -10.5537828665
4given(-0.10409925852, -0.727959879828, 0.67767083288), (0.730290211615, -0.518495712439, -0.444790291038), (0.675158908106, 0.448594036455, 0.585596993898)-5.93661105062, 11.9476008842, 31.6590996957
5given(0.172692832678, -0.904321517718, -0.39035852512), (-0.685314763432, -0.394973618413, 0.611832914921), (-0.707474989356, 0.161859301093, -0.687953999978)29.9885181956, -28.112514194, 67.3347838819

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Components

#1: Protein
Conotoxin Mu8.1


Mass: 10203.572 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus mucronatus (invertebrata) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.08 Å3/Da / Density % sol: 60.05 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.02 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 22% w/v Polyacrylic acid sodium salt 5,100)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1.7712 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.12→48.97 Å / Num. obs: 41056 / % possible obs: 97.3 % / Redundancy: 6.3 % / Biso Wilson estimate: 44.59 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.09074 / Rpim(I) all: 0.0385 / Rrim(I) all: 0.0988 / Net I/σ(I): 9.75
Reflection shellResolution: 2.12→2.196 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.8116 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 3498 / CC1/2: 0.676 / CC star: 0.898 / Rpim(I) all: 0.4409 / Rrim(I) all: 0.9292 / % possible all: 83.17

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PX1

7px1


Resolution: 2.12→48.97 Å / SU ML: 0.2787 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.7086
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2336 3999 5.08 %
Rwork0.2172 74684 -
obs0.2181 41056 94.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.32 Å2
Refinement stepCycle: LAST / Resolution: 2.12→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4070 0 90 123 4283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00344244
X-RAY DIFFRACTIONf_angle_d0.77995744
X-RAY DIFFRACTIONf_chiral_restr0.0345646
X-RAY DIFFRACTIONf_plane_restr0.0033704
X-RAY DIFFRACTIONf_dihedral_angle_d18.1409622
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.665472377097
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.698840043164
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.430791564789
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.554324052121
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.704506988127
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)
10.3758279362590.0305407988889-0.0331632998860.1265764891680.01160003492230.0945737827224-0.247586822145-0.352523511233-0.935494003315-0.336030978611-0.158341336821-0.1102452758870.5736206500710.1398863483930.002367902122870.569643554271-0.01677527308730.1056002756711.251367303970.2732309704040.601616185431-7.22291150688-11.265690486460.0448057941
21.776862243760.318144947532-0.008298915773352.25127699212-1.669966471451.238981159110.374059716543-0.275190399283-0.4016781628620.01937821267510.1341775721370.01990450533570.4846021339360.2122760257050.001889246451220.5868058203340.0241079663724-0.08871287678790.5560678471880.05121921125830.68373599358114.4380419501-15.877523981354.2784368111
30.0754664834862-0.141525700199-0.04101935663350.2063124427760.09081671026190.08243944154440.549133992789-0.56519085893-0.7584406423070.08501862358590.07225314627480.08500040679250.487574802115-0.5296233874580.005057281228940.656034416218-0.127238993565-0.08127819640250.7039180602860.3443248779740.7112337748723.94949682341-18.883918540356.4338424164
40.365295733726-0.0253049548486-0.04444736372610.002681105679310.02011481392890.2028954726410.213636085328-0.447882142885-0.5774320067760.05805698858070.1415999969590.188503840690.564905047686-0.3208087798450.4908400355490.695980384581-0.302285152198-0.1992630761020.6581455742450.8512078339760.9283192187186.09507795419-26.889054019561.6521825755
50.07326801204740.00628862909233-0.003461592094340.1377496117540.006070200088510.05849141619220.12731488203-0.507946959608-0.5753425047890.08839646604160.354249018751.383248862651.20018061256-0.7217503316460.002169165050370.694187419038-0.261027490323-0.166040392950.8588046817190.2419449689540.994891603104-3.18913388311-24.096811106852.0206555099
60.6750059810060.0827583449638-0.3535600901461.08256244448-0.1326657501630.855502645366-0.1264778727810.2095411118540.1449729910010.1485297380570.0513748313739-0.08719577773690.4146280053790.7669127258020.0002473328904110.639145581540.01107793973460.018290184750.3886498988070.02966572394980.6042191594020.7472675796478.4233994957419.3125071515
72.253454264480.263099745102-0.580586905350.607742785926-0.9021567193143.37273887985-0.06806499576970.1833605218630.2652941161430.08948947612670.1355211794180.0740445949568-0.493554335227-0.0758451677574.93247857663E-50.6267025781350.01886265571540.01499717600820.40259627498-0.004766352268470.576285934489-2.3881394361115.163797543522.3965076702
80.169650385368-0.570766981044-0.02675367505312.186092841920.1476076226950.964384691947-0.192058736791-0.169731798126-0.2432024126040.3517999326250.1861244006190.0143531342874-0.257976297234-0.413778557347-1.33110733902E-50.5046279642270.04542005758760.05754582171470.759536895727-0.08759338598480.453874057455-6.7018574985211.853300785242.4912783765
92.807665974540.0533824725274-0.1566478209391.07515672532-0.8010550933922.70308489057-0.0714619630324-0.2370559647180.3172438618570.3709408076750.1430794507360.000153769978119-0.620619152101-0.3951480211820.001492405837380.6798410760080.1191876844820.02305547291870.586267746965-0.04330253725130.561565509593-8.3196678455217.957991758436.1222224222
101.90335277166-0.0973863015278-0.5144991714821.395997464591.36169741861.384101396640.1615842546520.07293108572490.219788112505-0.1437998381680.1820046916230.052632790712-0.3137068881950.6345958227570.001393618067850.493238536757-0.08107584065390.04334873714730.7620351796610.01186182702990.5531534361887.10718717726.210930873085.16972011262
111.521883446020.8061503627580.06812099305142.4352404592-0.2494685570352.11864337222-0.1140924783590.0278143367658-0.1163214844530.02393471028160.206371090139-0.199862150422-0.2968396236960.684904529834-0.0001028875613060.4642525224870.009136313789470.01092207242890.682756229361-0.03988351928360.5091322424437.52990232181.29317132905-1.75675802077
121.759452511321.297686348570.5002537775521.688526629941.185556906171.177985948030.09754549047690.1957910597240.2463053961890.043038201948-0.3064120344570.064279207792-0.1208684718430.2549897152774.25072265404E-50.5573777032940.000347489424485-0.01060780659980.646590602368-0.009471727204650.599705633557-11.5704491643-6.59284739512-3.52196766799
130.569564343770.10457480236-0.3451980940110.6836170394380.4288514445560.5721681700780.01773499592670.0352505286478-0.085090259011-0.002360554639760.0572962580918-0.01591388470050.17250853343-0.136889910696-4.21022780029E-50.512785935295-0.01384892579310.07093342764210.5325625650080.00964505878270.56854089649-8.05059596362-1.427302207072.56070858512
140.2508617310720.1855552133950.09350902972940.165797218667-0.004375587607180.1262835373630.1228167499370.00593170715502-0.530612422677-0.1129988919770.252992466369-0.2811584802790.4111495252520.819943944866-0.0004068061650670.571446190290.01794186906270.01981538353140.562637726769-0.06190681665710.543828087014-1.07564229016-8.22604247987-6.44795400604
150.1348783261140.2166572918850.04873451376080.3280466463030.01807334301970.1643936345350.1251208381730.123194532608-0.401904401081-0.189522239550.0865914757871-0.4074026399880.4293923037210.5005141031229.21808054788E-50.616567823810.149704850341-0.07468495000230.68285931239-0.1494465174690.695025235648-0.820586832311-14.827814595-8.8828568001
160.844663311522-0.02558333084160.07207653641881.34159281892-0.559211529270.313987206983-0.0782443818352-0.2090151987810.440199696809-0.1546240775440.220067998756-0.283457899909-0.449346590152-0.378702939808-0.0004199713528950.5089785236170.101847645583-0.007152252655970.7410915388020.05014589858070.5374540491970.703835649185-0.27959645572647.9823363563
170.00318590775007-0.01536184089230.02438243676870.0520914305859-0.0954735565090.1680563535630.1853973785010.459471015338-0.442232388233-0.7903435162050.372864801232-0.1553716157921.18588416150.06462167512370.06982950809420.8732645942170.049403093952-0.01576393920680.72843333301-0.06252079663120.4529418821473.23194817143-9.2289593996634.3443995103
180.488096757160.267973928533-0.08675150199290.378829381771-0.07981606814830.01356205962870.08931644506290.08577734738360.237001879477-0.2437326232350.21495378387-0.161672333189-0.247351516685-0.240657254316-0.0004880587339720.52374927550.00492202576208-0.01342207773120.6008458774970.03359973613240.6106904560348.73092570986-4.5808924145148.8732361671
190.328906182459-0.1099055939670.1527816230520.754798665474-0.4309594704890.2714784878550.16021297251-0.633022654398-0.570841961626-0.1070474297040.4159412212630.197863531074-0.0474613197305-0.673699353433-0.0008337694771480.467725273675-0.0577490464839-0.00476167476960.7107471314910.1336670772340.566176058209-6.62519611999-8.0124517029749.8576990936
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid 79 through 89 )EI79 - 8975 - 85
22chain 'F' and (resid 5 through 48 )FK5 - 481 - 44
33chain 'F' and (resid 49 through 63 )FK49 - 6345 - 59
44chain 'F' and (resid 64 through 78 )FK64 - 7860 - 74
55chain 'F' and (resid 79 through 89 )FK79 - 8975 - 85
66chain 'A' and (resid 6 through 24 )AA6 - 241 - 19
77chain 'A' and (resid 25 through 89 )AA25 - 8920 - 84
88chain 'B' and (resid 6 through 29 )BC6 - 291 - 24
99chain 'B' and (resid 30 through 89 )BC30 - 8925 - 84
1010chain 'C' and (resid 5 through 29 )CE5 - 291 - 25
1111chain 'C' and (resid 30 through 89 )CE30 - 8926 - 85
1212chain 'D' and (resid 5 through 29 )DG5 - 291 - 25
1313chain 'D' and (resid 30 through 48 )DG30 - 4826 - 44
1414chain 'D' and (resid 49 through 63 )DG49 - 6345 - 59
1515chain 'D' and (resid 64 through 89 )DG64 - 8960 - 85
1616chain 'E' and (resid 5 through 24 )EI5 - 241 - 20
1717chain 'E' and (resid 25 through 29 )EI25 - 2921 - 25
1818chain 'E' and (resid 30 through 48 )EI30 - 4826 - 44
1919chain 'E' and (resid 49 through 78 )EI49 - 7845 - 74

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