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- PDB-7pgb: NaV_Ae1/Sp1CTD_pore-SAT09 complex -

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Basic information

Entry
Database: PDB / ID: 7pgb
TitleNaV_Ae1/Sp1CTD_pore-SAT09 complex
Components
  • (SAT09 fab fragment, ...) x 2
  • Ion transport protein,Voltage-gated sodium channelIon transporter
KeywordsMEMBRANE PROTEIN / ion channel membrane protein transport protein antibody complex
Function / homology
Function and homology information


monoatomic cation channel activity / membrane => GO:0016020 / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
4-NITROBENZOIC ACID / BENZENE HEXACARBOXYLIC ACID / DODECANE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / PENTANE / N-OCTANE / HEXADECANE / Voltage-gated sodium channel / Ion transport protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Alkalilimnicola ehrlichii (bacteria)
Ruegeria pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsLolicato, M. / Arrigoni, C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2022
Title: Quaternary structure independent folding of voltage-gated ion channel pore domain subunits.
Authors: Arrigoni, C. / Lolicato, M. / Shaya, D. / Rohaim, A. / Findeisen, F. / Fong, L.K. / Colleran, C.M. / Dominik, P. / Kim, S.S. / Schuermann, J.P. / DeGrado, W.F. / Grabe, M. / Kossiakoff, A.A. / Minor Jr., D.L.
History
DepositionAug 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 29, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: SAT09 fab fragment, heavy chain
L: SAT09 fab fragment, light chain
c: Ion transport protein,Voltage-gated sodium channel
A: SAT09 fab fragment, heavy chain
B: SAT09 fab fragment, light chain
C: Ion transport protein,Voltage-gated sodium channel
R: SAT09 fab fragment, heavy chain
S: SAT09 fab fragment, light chain
T: Ion transport protein,Voltage-gated sodium channel
U: SAT09 fab fragment, heavy chain
V: SAT09 fab fragment, light chain
W: Ion transport protein,Voltage-gated sodium channel
X: SAT09 fab fragment, heavy chain
Y: SAT09 fab fragment, light chain
Z: Ion transport protein,Voltage-gated sodium channel
a: SAT09 fab fragment, heavy chain
b: SAT09 fab fragment, light chain
d: Ion transport protein,Voltage-gated sodium channel
m: SAT09 fab fragment, heavy chain
n: SAT09 fab fragment, light chain
l: Ion transport protein,Voltage-gated sodium channel
p: SAT09 fab fragment, heavy chain
q: SAT09 fab fragment, light chain
o: Ion transport protein,Voltage-gated sodium channel
f: SAT09 fab fragment, heavy chain
g: SAT09 fab fragment, light chain
i: SAT09 fab fragment, heavy chain
k: SAT09 fab fragment, light chain
h: Ion transport protein,Voltage-gated sodium channel
e: Ion transport protein,Voltage-gated sodium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)660,553107
Polymers643,30230
Non-polymers17,25177
Water1629
1
H: SAT09 fab fragment, heavy chain
L: SAT09 fab fragment, light chain
c: Ion transport protein,Voltage-gated sodium channel
R: SAT09 fab fragment, heavy chain
S: SAT09 fab fragment, light chain
T: Ion transport protein,Voltage-gated sodium channel
X: SAT09 fab fragment, heavy chain
Y: SAT09 fab fragment, light chain
Z: Ion transport protein,Voltage-gated sodium channel
f: SAT09 fab fragment, heavy chain
g: SAT09 fab fragment, light chain
i: SAT09 fab fragment, heavy chain
k: SAT09 fab fragment, light chain
h: Ion transport protein,Voltage-gated sodium channel
e: Ion transport protein,Voltage-gated sodium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,85857
Polymers321,65115
Non-polymers9,20742
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: SAT09 fab fragment, heavy chain
B: SAT09 fab fragment, light chain
C: Ion transport protein,Voltage-gated sodium channel
U: SAT09 fab fragment, heavy chain
V: SAT09 fab fragment, light chain
W: Ion transport protein,Voltage-gated sodium channel
a: SAT09 fab fragment, heavy chain
b: SAT09 fab fragment, light chain
d: Ion transport protein,Voltage-gated sodium channel
m: SAT09 fab fragment, heavy chain
n: SAT09 fab fragment, light chain
l: Ion transport protein,Voltage-gated sodium channel
p: SAT09 fab fragment, heavy chain
q: SAT09 fab fragment, light chain
o: Ion transport protein,Voltage-gated sodium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,69550
Polymers321,65115
Non-polymers8,04435
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)200.865, 200.865, 327.727
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
12
22
32
42
52
62
72
82
92
102
13
23
33
43
53
63
73
83
93
103

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain 'A' and (resid 1 through 102 or resid 104 through 223))
221(chain 'H' and (resid 1 through 102 or resid 104 through 223))
331(chain 'R' and (resid 1 through 102 or resid 104 through 223))
441(chain 'U' and (resid 1 through 102 or resid 104 through 223))
551(chain 'X' and (resid 1 through 102 or resid 104 through 223))
661(chain 'a' and (resid 1 through 102 or resid 104 through 223))
771(chain 'f' and (resid 1 through 102 or resid 104 through 223))
881(chain 'i' and (resid 1 through 102 or resid 104 through 223))
991(chain 'm' and (resid 1 through 102 or resid 104 through 223))
10101(chain 'p' and (resid 1 through 102 or resid 104 through 223))
1112chain 'B'
2122chain 'L'
3132chain 'S'
4142chain 'V'
5152chain 'Y'
6162chain 'b'
7172chain 'g'
8182chain 'k'
9192chain 'n'
10202chain 'q'
1213(chain 'C' and (resid 148 through 149 or (resid 150...
2223(chain 'T' and (resid 148 through 237 or resid 239...
3233(chain 'W' and (resid 148 through 237 or resid 239...
4243(chain 'Z' and (resid 148 through 237 or resid 239...
5253(chain 'c' and (resid 148 through 149 or (resid 150...
6263(chain 'd' and (resid 148 through 237 or resid 239...
7273(chain 'e' and (resid 148 through 237 or resid 239...
8283(chain 'h' and (resid 148 through 237 or resid 239...
9293(chain 'l' and (resid 148 through 237 or resid 239...
10303(chain 'o' and (resid 148 through 237 or resid 239...

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.000626466020413, -0.999999641869, 0.000569036121804), (-0.999999803011, 0.000626443739973), (-0.000569060649931, -0.999999837325)-100.532628365, -100.474085117, -61.2500556348
2given(0.948745897957, -0.314279277948, 0.0333130089097), (-0.314579167384, -0.949222629179, 0.00404322911828), (0.0303507587753, -0.0143155756463, -0.999436789265)4.30330580401, 22.5282019262, -56.7960535756
3given(0.313708832771, -0.948997481344, -0.0314729827754), (0.949428416849, 0.313964884443, -0.00342529076515), (0.0131320037091, -0.0288068002421, 0.999498733735)-61.4037889121, 149.304218845, 2.60638209999
4given(-0.954401517654, -0.298520440668, -0.00181372623702), (-0.298421946477, 0.953891041341, 0.0321904195568), (-0.00787940102244, 0.031263840993, -0.999480108499)-251.677035866, -37.7537940105, -63.2978087954
5given(0.298588023215, 0.954380538702, 0.00172619206961), (-0.95387551387, 0.298487968228, -0.0320380533632), (-0.0310917421913, 0.00791960667393, 0.999485159168)-125.722039739, -105.544385979, -4.34909549185
6given(0.589795014234, 0.806926863788, 0.0317943026657), (0.806904582882, -0.590441936105, 0.0168319402639), (0.0323548343917, 0.015727574083, -0.99935269455)-80.4591909746, 161.248574326, -57.6654524566
7given(-0.5838020347, 0.811442824881, 0.0271242737915), (0.811547299574, 0.582246412715, 0.0487862217689), (0.0237942184949, 0.0504941266825, -0.998440873731)-238.1733361, 123.460476514, -59.7390818598
8given(-0.807364062565, -0.589220466418, -0.0313450543512), (0.589883357803, -0.807267495273, -0.018889554321), (-0.0141737315078, -0.0337406732279, 0.999330111778)-222.715687766, 138.325490365, -1.08438294836
9given(-0.812034244456, 0.58295583522, -0.0276202826491), (-0.581421840321, -0.812177647377, -0.0481260085372), (-0.0504879136845, -0.0230209314132, 0.998459316792)-262.831426294, -19.3637337878, -5.98192133369
10given(0.000657841950081, -0.999999750728, -0.00025649013811), (-0.999999745539, -0.000657771117148, -0.00027614902684), (0.000275980246199, 0.000256671735258, -0.999999928977)-100.337387088, -100.399632926, -61.265455663
11given(0.9506581799, -0.30907225612, 0.0268954547362), (-0.309300894194, -0.950952620374, 0.00469794152866), (0.0241242997702, -0.0127849247426, -0.999627212445)4.49276056396, 23.4631736306, -57.939891235
12given(0.309615025152, -0.950457696955, -0.0277254846285), (0.950778181003, 0.309843241151, -0.00424457778358), (0.0126248456445, -0.0250466007853, 0.999606563134)-61.5830400142, 149.717657249, 2.22282765411
13given(-0.95409897422, -0.299489221739, -0.00116338043647), (-0.299380032817, 0.953630769939, 0.0309830691846), (-0.00816965989583, 0.0299092074005, -0.999519232416)-251.543605231, -37.8401926207, -63.2858118217
14given(0.298738531981, 0.954334451784, 0.00102159108769), (-0.9538459471, 0.298619537484, -0.0316903934065), (-0.0305483012765, 0.00849270108558, 0.99949721126)-125.702262964, -105.51305951, -4.32088215669
15given(0.589221596192, 0.80727327823, 0.0335822101344), (0.807187923047, -0.589971540733, 0.0195253171965), (0.0355748150759, 0.0156024158851, -0.999245213724)-80.5117961861, 161.316057515, -57.2721910674
16given(-0.586114073467, 0.809852173736, 0.0246931079391), (0.809849184592, 0.58463500089, 0.048437732705), (0.02479094794, 0.0483877301547, -0.998520924403)-238.382392181, 123.210376138, -59.5951079927
17given(-0.807820465311, -0.58850264631, -0.0330262185505), (0.589242541469, -0.807704579991, -0.0201628069619), (-0.014809562729, -0.0357483810557, 0.999251084615)-222.876980011, 138.226866388, -1.09122302198
18given(-0.810467752346, 0.585208715252, -0.0259380415574), (-0.583697071236, -0.810522975837, -0.0484792189559), (-0.0493938400721, -0.0241508847321, 0.998487347606)-262.512944219, -19.7030594803, -5.88098434564
19given(0.946867858336, -0.318504447132, 0.0446785855496), (-0.318645327991, -0.947865051001, -0.00412311039995), (0.0436624987691, -0.0103325818326, -0.998992904857)4.08327370762, 21.7785918655, -54.887187931
20given(0.316025039543, -0.948012565495, -0.0374212512612), (0.948750728169, 0.315759134103, 0.0129701591932), (-0.000479771996318, -0.039602334455, 0.999215404667)-61.5339718835, 150.098446601, 1.34148248358
21given(-0.951664976673, -0.3067973617, 0.0144620547602), (-0.306419915519, 0.951604806868, 0.0235611315188), (-0.0209906538156, 0.0179908420794, -0.999617787984)-250.988303778, -38.5494004662, -64.2697185172
22given(-0.010881090961, -0.999824263047, 0.0152658076034), (-0.999858687586, 0.0110745734934, 0.0126474772104), (-0.0128143168895, -0.0151260320053, -0.999803478909)-102.11425586, -101.07242025, -62.3621824264
23given(0.307599390185, 0.951515772129, 0.00059207083495), (-0.950968870623, 0.30744357009, -0.0337143636416), (-0.0322617771235, 0.00980747676341, 0.999431333878)-124.358054061, -105.418973166, -4.57324158574
24given(0.585463804245, 0.809247335543, 0.0484859137912), (0.809219444931, -0.586960649782, 0.0253196673136), (0.0489491967746, 0.0244119954975, -0.998502894643)-81.1089119107, 161.468715436, -55.4549548379
25given(-0.587792847372, 0.808544723342, 0.0274772439302), (0.808786687578, 0.58648990199, 0.0435165354799), (0.0190699390408, 0.0478019373996, -0.998674777996)-238.561793288, 123.038188783, -60.2678519903
26given(-0.807685284941, -0.587043214156, -0.0549976836252), (0.588630707259, -0.808207368438, -0.0177409152734), (-0.0340348492288, -0.0467024016177, 0.998328861008)-224.336887223, 138.275965453, -2.92949697655
27given(-0.809143269597, 0.586640832261, -0.0337594903566), (-0.584941804337, -0.809607020293, -0.0487807157744), (-0.0559486800944, -0.0197232506523, 0.998238818409)-262.908805275, -19.9141090286, -6.74299567441

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Components

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Protein , 1 types, 10 molecules cCTWZdlohe

#3: Protein
Ion transport protein,Voltage-gated sodium channel / Ion transporter


Mass: 16121.689 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alkalilimnicola ehrlichii (strain ATCC BAA-1101 / DSM 17681 / MLHE-1) (bacteria), (gene. exp.) Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3) (bacteria)
Strain: ATCC BAA-1101 / DSM 17681 / MLHE-1, ATCC 700808 / DSM 15171 / DSS-3
Gene: Mlg_0322, SPO0030 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0ABW0, UniProt: F7IVA8

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Antibody , 2 types, 20 molecules HARUXampfiLBSVYbnqgk

#1: Antibody
SAT09 fab fragment, heavy chain


Mass: 24885.594 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody
SAT09 fab fragment, light chain


Mass: 23322.895 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 11 types, 86 molecules

#4: Chemical...
ChemComp-4NB / 4-NITROBENZOIC ACID / PARA NITROBENZOIC ACID / 4-Nitrobenzoic acid


Mass: 167.119 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C7H5NO4
#5: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#6: Chemical
ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C8H18
#7: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#8: Chemical
ChemComp-LNK / PENTANE / Pentane


Mass: 72.149 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C5H12
#9: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#10: Chemical ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26
#11: Chemical ChemComp-R16 / HEXADECANE / Hexadecane


Mass: 226.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34
#12: Chemical ChemComp-BHC / BENZENE HEXACARBOXYLIC ACID / Mellitic acid


Mass: 342.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H6O12
#13: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#14: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 5.14 Å3/Da / Density % sol: 76.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12-14% PEG4000 0.1M NaCl, 0.1M MgCl2, 1 M Na acetate, pH 3.2-3.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→15 Å / Num. obs: 147489 / % possible obs: 98.47 % / Redundancy: 7 % / Biso Wilson estimate: 156.76 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.166 / Net I/σ(I): 9.3
Reflection shellResolution: 3.6→3.73 Å / Rmerge(I) obs: 1 / Num. unique obs: 14754 / CC1/2: 0.13

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Processing

Software
NameVersionClassification
Coot1.17.1_3660model building
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HK7

5hk7


Resolution: 3.6→15 Å / SU ML: 0.6014 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.0704
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2321 7391 5.02 %
Rwork0.207 139933 -
obs0.2082 147324 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 190.33 Å2
Refinement stepCycle: LAST / Resolution: 3.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41538 0 1197 9 42744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00343781
X-RAY DIFFRACTIONf_angle_d0.734359411
X-RAY DIFFRACTIONf_chiral_restr0.04756552
X-RAY DIFFRACTIONf_plane_restr0.00587394
X-RAY DIFFRACTIONf_dihedral_angle_d11.483915348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.640.35812420.37774579X-RAY DIFFRACTION98.81
3.64-3.680.41492540.38284673X-RAY DIFFRACTION99.52
3.68-3.730.37722340.39454674X-RAY DIFFRACTION99.68
3.73-3.770.39022800.37774607X-RAY DIFFRACTION99.96
3.77-3.820.38532360.36574638X-RAY DIFFRACTION99.98
3.82-3.870.36382620.34724698X-RAY DIFFRACTION99.96
3.87-3.930.37362560.34124598X-RAY DIFFRACTION99.96
3.93-3.990.3822380.34984647X-RAY DIFFRACTION100
3.99-4.050.3542500.32284702X-RAY DIFFRACTION99.98
4.05-4.110.32062250.30044652X-RAY DIFFRACTION100
4.11-4.180.29682210.2764757X-RAY DIFFRACTION99.98
4.18-4.260.29742550.24334586X-RAY DIFFRACTION100
4.26-4.340.25732260.22994665X-RAY DIFFRACTION100
4.34-4.420.26482280.2184685X-RAY DIFFRACTION100
4.42-4.510.2292350.19664710X-RAY DIFFRACTION100
4.52-4.620.21932620.19454605X-RAY DIFFRACTION100
4.62-4.730.2082370.18474704X-RAY DIFFRACTION100
4.73-4.850.22572410.19034657X-RAY DIFFRACTION100
4.85-4.990.24932860.18244655X-RAY DIFFRACTION100
4.99-5.140.22052340.18644683X-RAY DIFFRACTION99.92
5.15-5.320.19522270.18654634X-RAY DIFFRACTION100
5.32-5.520.192690.1734703X-RAY DIFFRACTION99.96
5.52-5.760.19942480.17644690X-RAY DIFFRACTION100
5.76-6.050.26232530.18794655X-RAY DIFFRACTION100
6.05-6.40.2062170.18834713X-RAY DIFFRACTION100
6.4-6.850.21892570.18994641X-RAY DIFFRACTION100
6.85-7.460.20212350.1864724X-RAY DIFFRACTION100
7.46-8.370.17292560.16444677X-RAY DIFFRACTION100
8.37-100.17572690.15164652X-RAY DIFFRACTION99.98
10-150.18892580.17124669X-RAY DIFFRACTION98.88

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