[English] 日本語
Yorodumi
- PDB-7egr: Co-crystal structure of Ac-AChBPP in complex with RgIA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7egr
TitleCo-crystal structure of Ac-AChBPP in complex with RgIA
Components
  • (Soluble acetylcholine ...) x 3
  • RgIA
KeywordsTOXIN / acetylcholine binding protein / nicotinic acetylcholine receptors / conotoxin / molecular dynamics simulation
Function / homology
Function and homology information


excitatory extracellular ligand-gated monoatomic ion channel activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / postsynapse / neuron projection / identical protein binding / membrane / metal ion binding
Similarity search - Function
Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
Conus regius (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsWang, X.Q. / Pan, S. / Fan, Y.X. / Xue, Y. / Zhu, X.P. / Luo, S.L.
CitationJournal: To Be Published
Title: Co-crystal structure of Ac-AChBPP in complex with RgIA
Authors: Wang, X.Q. / Pan, S. / Fan, Y.X. / Xue, Y. / Zhu, X.P. / Luo, S.L.
History
DepositionMar 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Soluble acetylcholine receptor
B: Soluble acetylcholine receptor
C: Soluble acetylcholine receptor
D: Soluble acetylcholine receptor
E: Soluble acetylcholine receptor
F: Soluble acetylcholine receptor
G: Soluble acetylcholine receptor
H: Soluble acetylcholine receptor
I: Soluble acetylcholine receptor
J: Soluble acetylcholine receptor
K: RgIA
L: RgIA
M: RgIA
N: RgIA
O: RgIA
P: RgIA
R: RgIA
Q: RgIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,85228
Polymers245,60918
Non-polymers24310
Water9,116506
1
A: Soluble acetylcholine receptor
B: Soluble acetylcholine receptor
C: Soluble acetylcholine receptor
D: Soluble acetylcholine receptor
E: Soluble acetylcholine receptor
K: RgIA
L: RgIA
M: RgIA
N: RgIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,70615
Polymers122,5609
Non-polymers1466
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Soluble acetylcholine receptor
G: Soluble acetylcholine receptor
H: Soluble acetylcholine receptor
I: Soluble acetylcholine receptor
J: Soluble acetylcholine receptor
O: RgIA
P: RgIA
R: RgIA
Q: RgIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,14613
Polymers123,0499
Non-polymers974
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)206.271, 135.955, 132.067
Angle α, β, γ (deg.)90.000, 101.160, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Soluble acetylcholine ... , 3 types, 10 molecules ADGHIJBCEF

#1: Protein
Soluble acetylcholine receptor


Mass: 23378.113 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Production host: Baculovirus expression vector pCTdual / References: UniProt: Q8WSF8
#2: Protein Soluble acetylcholine receptor


Mass: 23133.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Production host: Baculovirus expression vector pCTdual / References: UniProt: Q8WSF8
#3: Protein Soluble acetylcholine receptor


Mass: 23220.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Production host: Baculovirus expression vector pCTdual / References: UniProt: Q8WSF8

-
Protein/peptide , 1 types, 8 molecules KLMNOPRQ

#4: Protein/peptide
RgIA


Mass: 1578.868 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus regius (invertebrata) / Production host: Synthesium tursionis (invertebrata)

-
Non-polymers , 2 types, 516 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.8 M Magnesium sulfate hydrate, 0.1 M Sodium acetate trihydrate pH 4.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 121060 / % possible obs: 98.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.063 / Rrim(I) all: 0.127 / Χ2: 0.924 / Net I/σ(I): 8.9 / Num. measured all: 468524
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.563.70.79279380.6720.4660.9230.90897.2
2.56-2.6240.64781690.730.3690.7470.88999.7
2.62-2.6940.57180600.7750.3270.660.97299.7
2.69-2.7740.44781180.8510.2540.5160.9499.7
2.77-2.8640.35381170.9080.2030.4090.95499.4
2.86-2.9640.29380910.9390.1680.3391.01199.4
2.96-3.083.90.21281130.9560.1230.2461.03899.2
3.08-3.223.90.16880450.9710.0970.1951.10999.2
3.22-3.393.80.12280630.9840.0720.1421.13898.8
3.39-3.613.50.09177960.9910.0540.1061.12795.5
3.61-3.883.80.07679560.9930.0440.0881.03297.2
3.88-4.2740.05781860.9960.0320.0660.853100
4.27-4.8940.04581570.9970.0250.0510.64899.6
4.89-6.163.80.04681450.9970.0260.0530.71398.7
6.16-503.70.03581060.9990.020.0410.55797.5

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CO5

5co5


Resolution: 2.503→35.401 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2208 5892 4.87 %
Rwork0.1719 115130 -
obs0.1743 121022 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.37 Å2 / Biso mean: 41.7378 Å2 / Biso min: 17.08 Å2
Refinement stepCycle: final / Resolution: 2.503→35.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17164 0 10 506 17680
Biso mean--42.97 39.78 -
Num. residues----2158
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.503-2.53130.31691910.2617335286
2.5313-2.56110.32722020.2571381399
2.5611-2.59230.28961890.23783869100
2.5923-2.62510.30372120.2263889100
2.6251-2.65970.2782170.23263825100
2.6597-2.69610.27772010.23233864100
2.6961-2.73460.27491740.22623907100
2.7346-2.77540.24211940.21473868100
2.7754-2.81880.27231890.2117389199
2.8188-2.86490.29371900.2073387299
2.8649-2.91430.26121950.2064384899
2.9143-2.96730.2621810.2014389599
2.9673-3.02430.25472280.1908382499
3.0243-3.0860.24122160.187385599
3.086-3.15310.27282100.1905384399
3.1531-3.22640.22451990.1823385099
3.2264-3.3070.22831970.1719385099
3.307-3.39640.22531870.1664383899
3.3964-3.49620.22591970.1635378798
3.4962-3.6090.20891900.1596367294
3.609-3.73780.20451790.16369194
3.7378-3.88730.22321940.15923911100
3.8873-4.0640.20042020.1513868100
4.064-4.27790.18161860.13543933100
4.2779-4.54540.14262080.12373903100
4.5454-4.89550.16851870.1234389899
4.8955-5.38670.19881930.1442388099
5.3867-6.16260.20381970.1691387298
6.1626-7.75070.18831980.1694378496
7.7507-35.4010.19981890.1765397899
Refinement TLS params.Method: refined / Origin x: -14.4882 Å / Origin y: -40.8139 Å / Origin z: 33.6165 Å
111213212223313233
T0.2314 Å2-0.0421 Å2-0.0036 Å2-0.2192 Å2-0.0067 Å2--0.181 Å2
L0.4779 °20.1608 °2-0.0436 °2-0.2597 °2-0.0196 °2--0.176 °2
S0.0095 Å °0.0213 Å °-0.0279 Å °0.0185 Å °-0.0095 Å °0.027 Å °0.0208 Å °-0.0303 Å °-0.0004 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA19 - 224
2X-RAY DIFFRACTION1allB20 - 223
3X-RAY DIFFRACTION1allC20 - 223
4X-RAY DIFFRACTION1allD19 - 224
5X-RAY DIFFRACTION1allE19 - 223
6X-RAY DIFFRACTION1allF19 - 223
7X-RAY DIFFRACTION1allG19 - 224
8X-RAY DIFFRACTION1allH19 - 224
9X-RAY DIFFRACTION1allI19 - 224
10X-RAY DIFFRACTION1allJ19 - 224
11X-RAY DIFFRACTION1allK401 - 413
12X-RAY DIFFRACTION1allL401 - 413
13X-RAY DIFFRACTION1allM401 - 413
14X-RAY DIFFRACTION1allN401 - 413
15X-RAY DIFFRACTION1allO401 - 413
16X-RAY DIFFRACTION1allP401 - 413
17X-RAY DIFFRACTION1allR401 - 413
18X-RAY DIFFRACTION1allQ401 - 413
19X-RAY DIFFRACTION1allS2 - 508
20X-RAY DIFFRACTION1allT1 - 10

+
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