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- PDB-8e0e: nbF3:CaV beta subunit 2a complex -

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Basic information

Entry
Database: PDB / ID: 8e0e
TitlenbF3:CaV beta subunit 2a complex
Components
  • Nanobody nb.F3
  • Voltage-dependent L-type calcium channel subunit beta-2
KeywordsTRANSPORT PROTEIN/IMMUNE SYSTEM / nanobody-CACNB2a complex / TRANSPORT PROTEIN / TRANSPORT PROTEIN-IMMUNE SYSTEM complex / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


regulation of monoatomic ion transmembrane transport / voltage-gated calcium channel complex / voltage-gated calcium channel activity / sarcolemma
Similarity search - Function
Voltage-dependent calcium channel, L-type, beta-2 subunit / CACNB2, SH3 domain / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / Voltage-dependent calcium channel, L-type, beta subunit / Voltage gated calcium channel subunit beta domain 4Aa N terminal / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...Voltage-dependent calcium channel, L-type, beta-2 subunit / CACNB2, SH3 domain / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / Voltage-dependent calcium channel, L-type, beta subunit / Voltage gated calcium channel subunit beta domain 4Aa N terminal / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Voltage-dependent L-type calcium channel subunit beta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNirwan, N. / Minor, D.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: Nat Commun / Year: 2022
Title: Selective posttranslational inhibition of Ca V beta 1 -associated voltage-dependent calcium channels with a functionalized nanobody.
Authors: Morgenstern, T.J. / Nirwan, N. / Hernandez-Ochoa, E.O. / Bibollet, H. / Choudhury, P. / Laloudakis, Y.D. / Ben Johny, M. / Bannister, R.A. / Schneider, M.F. / Minor Jr., D.L. / Colecraft, H.M.
History
DepositionAug 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Voltage-dependent L-type calcium channel subunit beta-2
B: Nanobody nb.F3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,71813
Polymers52,7212
Non-polymers99811
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-61 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.525, 144.525, 63.596
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#1: Protein Voltage-dependent L-type calcium channel subunit beta-2 / Calcium channel voltage-dependent subunit beta 2


Mass: 39425.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cacnb2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8I6AEJ4
#2: Antibody Nanobody nb.F3


Mass: 13294.556 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 224 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 3.64 Å3/Da / Density % sol: 66.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH7, 30%-40% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2→47.31 Å / Num. obs: 51357 / % possible obs: 99.94 % / Redundancy: 20 % / Biso Wilson estimate: 41.7 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.07368 / Net I/σ(I): 32.4
Reflection shellResolution: 2→2.071 Å / Num. unique obs: 5099 / CC1/2: 0.783 / CC star: 0.937 / % possible all: 99.96

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V2P

5v2p


Resolution: 2→47.31 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 2563 4.99 %
Rwork0.1974 48786 -
obs0.1986 51349 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.2 Å2 / Biso mean: 68.6459 Å2 / Biso min: 28.6 Å2
Refinement stepCycle: final / Resolution: 2→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 64 213 3767
Biso mean--78.09 54.29 -
Num. residues----443
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.040.36781820.383426482830
2.04-2.080.32331530.344826702823
2.08-2.130.33361450.314627122857
2.13-2.170.35711180.2826932811
2.17-2.230.29571430.260626912834
2.23-2.290.29661330.283527272860
2.29-2.360.2861250.233727162841
2.36-2.430.21651190.22827092828
2.43-2.520.28011440.247326842828
2.52-2.620.30661280.228727162844
2.62-2.740.27131610.230326862847
2.74-2.880.24731160.215627312847
2.88-3.060.21571390.2227042843
3.07-3.30.24381430.202427272870
3.3-3.630.19411640.183227032867
3.63-4.160.17931600.169727182878
4.16-5.240.16731300.150627572887
5.24-47.310.20651600.163927942954
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)
15.7168-2.9502-0.89244.68883.3546.9236-0.1666-0.1229-0.3880.6138-0.19270.85230.542-0.5340.39820.68330.08830.06510.36410.00490.9903-48.8031-30.912110.5747
24.7929-2.59-2.60324.93812.32665.0194-0.145-0.19010.02660.15450.10720.39510.043-0.08350.05160.26470.05260.01250.25590.01340.5028-35.6782-45.33775.442
33.27551.0717-0.12313.18341.05651.85680.1775-1.18990.10641.22280.19370.15030.50450.248-0.18440.71520.19030.03350.6590.09350.5619-31.1329-51.665317.0755
43.9649-1.25430.31163.43870.46952.5136-0.0054-0.16490.2966-0.1370.2671-0.5936-0.1970.4487-0.24640.2249-0.00130.05450.3665-0.03560.4553-12.5207-55.9176-6.0664
54.6511-2.19470.47955.18910.68612.59710.24050.2346-0.5445-0.36220.0276-0.31950.35160.3132-0.19520.32220.0637-0.04530.3261-0.04880.5269-18.1228-70.0204-12.8326
60.0575-0.6059-0.1292.34820.8880.10541.85241.60830.3333-2.017-2.00170.5121-0.4684-0.77360.1260.87790.3146-0.0620.7958-0.0150.9126-47.3358-32.6781-10.7054
71.7519-0.9805-0.15631.0242-1.18354.12530.3335-0.97541.21920.9503-0.0078-0.759-1.11520.8991-0.06610.6126-0.2146-0.13781.97-1.19621.6172-6.5725-34.450618.8775
82.89083.42152.98674.20474.1396.0266-0.1039-1.65040.1652.23070.4875-0.06270.92170.2896-0.33160.91380.349-0.2151.049-0.39820.8212-22.5788-43.126721.1992
91.65061.73030.93072.26131.61913.97040.0612-0.78341.7754-0.46560.7072-1.0072-0.87961.1579-0.48380.5193-0.12130.10680.7853-0.46781.4635-11.9766-34.9217.3894
105.85910.8614-1.21172.38722.03622.36530.2348-1.73791.98360.67880.881-1.3976-0.63421.5823-0.52880.5835-0.0195-0.02921.3905-0.77591.4594-8.0511-36.835213.3883
116.32744.41592.12633.45391.29761.06360.4335-0.59761.4586-0.14880.3783-0.9237-1.0930.749-0.16980.5841-0.16460.09490.7647-0.52531.368-16.6407-31.519811.9086
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 57 )A29 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 120 )A58 - 120
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 228 )A121 - 228
4X-RAY DIFFRACTION4chain 'A' and (resid 229 through 345 )A229 - 345
5X-RAY DIFFRACTION5chain 'A' and (resid 346 through 410 )A346 - 410
6X-RAY DIFFRACTION6chain 'A' and (resid 411 through 425 )A411 - 425
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 25 )B2 - 25
8X-RAY DIFFRACTION8chain 'B' and (resid 26 through 33 )B26 - 33
9X-RAY DIFFRACTION9chain 'B' and (resid 34 through 69 )B34 - 69
10X-RAY DIFFRACTION10chain 'B' and (resid 70 through 100 )B70 - 100
11X-RAY DIFFRACTION11chain 'B' and (resid 101 through 122 )B101 - 122

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