[English] 日本語
Yorodumi
- PDB-8e0e: nbF3:CaV beta subunit 2a complex -

+
Open data


ID or keywords:

Loading...

-
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


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 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 Domains / SH3 type barrels. ...Voltage-dependent calcium channel, L-type, beta-2 subunit / CACNB2, SH3 domain / 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 Domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleotide triphosphate hydrolases / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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)

-
Non-polymers , 5 types, 224 molecules

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


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


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more