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- PDB-8dam: nbF3:nbE8:CaV beta subunit 1b complex -

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Basic information

Entry
Database: PDB / ID: 8dam
TitlenbF3:nbE8:CaV beta subunit 1b complex
Components
  • Nanobody E8
  • Voltage-dependent L-type calcium channel subunit beta-1
  • nanobody F3
KeywordsTRANSPORT PROTEIN/IMMUNE SYSTEM / nanobody-CACNB1b complex / TRANSPORT PROTEIN / TRANSPORT PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Phase 0 - rapid depolarisation / Phase 2 - plateau phase / Presynaptic depolarization and calcium channel opening / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / positive regulation of muscle contraction / protein targeting to membrane / voltage-gated calcium channel complex / voltage-gated calcium channel activity / T-tubule ...Phase 0 - rapid depolarisation / Phase 2 - plateau phase / Presynaptic depolarization and calcium channel opening / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / positive regulation of muscle contraction / protein targeting to membrane / voltage-gated calcium channel complex / voltage-gated calcium channel activity / T-tubule / sarcoplasmic reticulum / calcium ion transmembrane transport / calcium ion transport / presynapse / plasma membrane
Similarity search - Function
Voltage-dependent calcium channel, L-type, beta-1 subunit / Voltage-dependent calcium channel, L-type, beta subunit / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / 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 ...Voltage-dependent calcium channel, L-type, beta-1 subunit / Voltage-dependent calcium channel, L-type, beta subunit / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Voltage-dependent L-type calcium channel subunit beta-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
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
DepositionJun 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 30, 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: Voltage-dependent L-type calcium channel subunit beta-1
B: nanobody F3
C: Nanobody E8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6218
Polymers69,1193
Non-polymers5025
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.358, 81.072, 93.332
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Voltage-dependent L-type calcium channel subunit beta-1 / CAB1 / Calcium channel voltage-dependent subunit beta 1


Mass: 41294.887 Da / Num. of mol.: 1 / Fragment: amino acids 58-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cacnb1, Cacnlb1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8R3Z5

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Antibody , 2 types, 2 molecules BC

#2: Antibody nanobody F3


Mass: 13445.397 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)
#3: Antibody Nanobody E8


Mass: 14378.789 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 , 3 types, 207 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 15-22% PEG3350, 0.15-0.25M Ammonium Sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2→48.69 Å / Num. obs: 41850 / % possible obs: 98.89 % / Redundancy: 12.7 % / Biso Wilson estimate: 34.77 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.53
Reflection shellResolution: 2→2.072 Å / Num. unique obs: 4114 / CC1/2: 0.813

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Processing

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

5v2p


Resolution: 2→48.69 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2268 1957 4.72 %
Rwork0.1932 39466 -
obs0.1948 41423 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.11 Å2 / Biso mean: 49.2386 Å2 / Biso min: 19.85 Å2
Refinement stepCycle: final / Resolution: 2→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4218 0 28 202 4448
Biso mean--70.07 44.64 -
Num. residues----541
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.30871310.26152787291899
2.05-2.110.28911410.240228022943100
2.11-2.170.25991260.224328412967100
2.17-2.240.27561320.2392766289898
2.24-2.320.41151160.31542454257088
2.32-2.410.24271550.214728182973100
2.41-2.520.23811220.220728462968100
2.52-2.650.25031680.213427942962100
2.65-2.820.25461670.204228122979100
2.82-3.040.23461600.199328292989100
3.04-3.340.21941170.186228993016100
3.34-3.830.17291270.172728763003100
3.83-4.820.18511300.149629163046100
4.82-48.690.21891650.188230263191100
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)
13.59752.1111-3.28513.5055-1.3748.49110.104-0.1439-0.3693-0.0641-0.00680.05970.5483-1.4536-0.29110.4012-0.0123-0.05710.63550.03740.4366-2.6999-0.84171.1777
23.831.5271-0.14142.97960.02322.22140.0364-0.0549-0.18070.081-0.01240.00780.1132-0.1136-0.02180.1910.0022-0.00260.19890.01690.143414.8095-9.1652-7.5756
33.7482-0.5049-0.14792.97770.6525.1780.08310.1171-0.1842-0.1953-0.2138-0.56540.4821.02880.10690.35680.06140.06470.46450.10660.41342.0138-2.558-20.4696
42.45010.586-2.58937.85330.73155.44060.25570.59530.5434-0.2346-0.10630.0655-0.4627-0.0834-0.24950.2746-0.0016-0.03630.31340.07170.244725.42676.3997-24.4883
53.11462.0952.36884.33894.32834.46710.7762-1.67710.30240.1305-0.65260.95311.0091-1.0157-0.06620.417-0.027-0.05440.40060.04570.406723.5333-14.263517.0707
62.38360.6597-0.2655.3467-1.43964.95290.19150.2911-0.03990.31840.1136-0.6137-0.10670.4287-0.26010.25880.0943-0.08770.4472-0.12910.387144.225-8.101419.3515
72.72740.978-0.22312.8333-0.12357.15360.24980.611-0.1231-0.26190.16120.7431.4787-0.4155-0.27440.5097-0.0037-0.09320.3653-0.03970.352125.8193-17.526212.0796
89.4392.18675.00171.91641.19283.6330.4844-0.6557-0.12970.6939-0.2778-0.02321.0489-0.1908-0.21180.3729-0.0167-0.0410.34970.00550.235423.4272-12.75816.0218
98.30620.4049-0.94658.65576.03219.25630.0328-0.48110.48170.8110.6689-0.446-0.26320.2862-0.59620.35130.0546-0.04110.293-0.04260.246629.67071.27818.154
106.7997-4.5669-3.27987.05220.84453.7670.07260.4379-0.0418-0.51870.1469-0.0408-0.22670.2318-0.22260.1859-0.01620.00320.23520.06910.153629.6555-6.09433.8393
114.47756.12434.21569.24574.05498.4756-0.0580.2729-0.2647-0.12050.0353-0.5193-0.25760.7427-0.01420.23110.01340.03460.3336-0.01430.273837.0423-4.37896.1964
125.58693.20624.6079.56244.84524.4097-0.04380.0746-0.7641-0.12050.2786-0.16760.56020.3205-0.37390.34490.0159-0.03190.27140.01110.262632.7269-16.2479.0052
137.6695-0.97971.2361.51711.86126.3451-0.2256-0.23720.59740.13410.1603-0.2716-0.39860.10220.05840.35920.0215-0.04450.2577-0.06830.352138.552-2.629116.8349
147.9645-6.36973.88085.2879-3.33252.38540.05360.23270.4329-0.5768-0.0144-0.12620.039-0.3990.05490.3682-0.0219-0.04570.2394-0.00680.181222.8776-3.13484.768
159.7176-0.08895.36722.6621-3.89498.5858-0.2003-0.31570.19230.07130.12030.4455-0.9845-0.94490.05950.37710.1306-0.04490.4314-0.10790.249721.5652-5.456814.2512
164.23543.16114.42252.85573.62945.03730.7283-0.62480.3630.9559-0.1029-0.9572-0.40430.3452-0.60880.3947-0.0012-0.0680.4228-0.14230.452440.9959-3.240123.5066
173.37721.63380.64037.0953-0.08713.86670.05652.84150.102-0.95730.20340.880.4038-1.396-0.36580.6342-0.0826-0.20850.7103-0.01490.46892.2408-27.5849-31.9127
184.9592-0.5137-2.55562.32110.84375.8506-0.09161.2181-0.1003-0.94490.0896-0.22550.0968-0.11690.00680.5485-0.06820.11840.6648-0.05320.379811.903-23.8783-34.5521
196.7708-2.913-1.38746.79185.46558.5896-0.32730.1955-1.08920.16210.21010.0130.77150.23260.10810.2872-0.04580.13290.3729-0.05160.376117.6351-26.5538-26.8962
206.6442-1.3372-5.10812.75433.87378.1498-0.04850.9816-0.0818-0.45650.1689-0.5025-0.34710.432-0.09820.3977-0.07060.14160.4579-0.02740.398722.036-20.623-30.6603
217.8613-0.2943-2.37134.89350.77175.6284-0.11380.80960.0905-0.91850.1753-0.6199-0.3945-0.1391-0.11840.4761-0.06540.13330.5592-0.11960.373216.5513-25.9801-34.4987
227.37394.73685.26416.83925.95488.7542-0.0610.2853-0.33290.16150.1473-0.26830.1373-0.0522-0.11250.2507-0.0080.02990.21880.01110.265713.1807-24.4864-17.5011
238.8149-4.6959-6.53872.50763.38695.36560.00981.4267-1.1016-0.9749-0.2139-0.5317-0.1632-0.98620.6070.7286-0.14350.36320.7578-0.3040.743514.7314-34.4783-37.7459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 70 through 98 )A70 - 98
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 231 )A99 - 231
3X-RAY DIFFRACTION3chain 'A' and (resid 232 through 393 )A232 - 393
4X-RAY DIFFRACTION4chain 'A' and (resid 394 through 419 )A394 - 419
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 8 )B2 - 8
6X-RAY DIFFRACTION6chain 'B' and (resid 9 through 20 )B9 - 20
7X-RAY DIFFRACTION7chain 'B' and (resid 21 through 29 )B21 - 29
8X-RAY DIFFRACTION8chain 'B' and (resid 30 through 36 )B30 - 36
9X-RAY DIFFRACTION9chain 'B' and (resid 37 through 46 )B37 - 46
10X-RAY DIFFRACTION10chain 'B' and (resid 47 through 58 )B47 - 58
11X-RAY DIFFRACTION11chain 'B' and (resid 59 through 74 )B59 - 74
12X-RAY DIFFRACTION12chain 'B' and (resid 75 through 83 )B75 - 83
13X-RAY DIFFRACTION13chain 'B' and (resid 84 through 97 )B84 - 97
14X-RAY DIFFRACTION14chain 'B' and (resid 98 through 106 )B98 - 106
15X-RAY DIFFRACTION15chain 'B' and (resid 107 through 116 )B107 - 116
16X-RAY DIFFRACTION16chain 'B' and (resid 117 through 123 )B117 - 123
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 8 )C1 - 8
18X-RAY DIFFRACTION18chain 'C' and (resid 9 through 34 )C9 - 34
19X-RAY DIFFRACTION19chain 'C' and (resid 35 through 58 )C35 - 58
20X-RAY DIFFRACTION20chain 'C' and (resid 59 through 74 )C59 - 74
21X-RAY DIFFRACTION21chain 'C' and (resid 75 through 100 )C75 - 100
22X-RAY DIFFRACTION22chain 'C' and (resid 101 through 120 )C101 - 120
23X-RAY DIFFRACTION23chain 'C' and (resid 121 through 128 )C121 - 128

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