[English] 日本語
Yorodumi
- PDB-7r23: Crystal structure of human Arc CTD in complex with two anti-Arc n... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7r23
TitleCrystal structure of human Arc CTD in complex with two anti-Arc nanobodies
Components
  • ARC
  • Chains: B
  • Chains: C
KeywordsSTRUCTURAL PROTEIN / capsid / nanobody / Gag homology
Function / homology
Function and homology information


positive regulation of AMPA receptor activity / modulation of chemical synaptic transmission / mRNA binding
Similarity search - Function
Activity-regulated cytoskeleton-associated protein / Activity-regulated cytoskeleton-associated protein, C-terminal domain / Activity-regulated cytoskeleton-associated protein, N-terminal domain / Arc C-lobe / Arc MA domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsMarkusson, S. / Kursula, P.
Funding support Norway, 1items
OrganizationGrant numberCountry
Norwegian Research Council249951 Norway
CitationJournal: To Be Published
Title: Crystal structure of human Arc CTD in complex with two anti-Arc nanobodies
Authors: Markusson, S. / Kursula, P.
History
DepositionFeb 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ARC
B: Chains: B
C: Chains: C


Theoretical massNumber of molelcules
Total (without water)48,9503
Polymers48,9503
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-14 kcal/mol
Surface area19250 Å2
Unit cell
Length a, b, c (Å)40.800, 61.640, 171.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein ARC


Mass: 21743.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CgPICR_014872 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3L7I2Q1
#2: Antibody Chains: B


Mass: 14078.622 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Antibody Chains: C


Mass: 13127.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M Na malonate, 0.2 M KBr

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.77→50 Å / Num. obs: 21261 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 66.76 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.251 / Net I/σ(I): 7.5
Reflection shellResolution: 2.77→2.84 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 849 / CC1/2: 0.324 / Rrim(I) all: 3.407 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TNO,6TN7

6tno

6tn7


Resolution: 2.77→42.99 Å / SU ML: 0.5141 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.7535
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3024 2107 10.03 %
Rwork0.2516 18891 -
obs0.2565 20998 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.55 Å2
Refinement stepCycle: LAST / Resolution: 2.77→42.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3126 0 0 0 3126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00193196
X-RAY DIFFRACTIONf_angle_d0.43254320
X-RAY DIFFRACTIONf_chiral_restr0.0375450
X-RAY DIFFRACTIONf_plane_restr0.0025557
X-RAY DIFFRACTIONf_dihedral_angle_d17.92661177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.830.43461220.41491091X-RAY DIFFRACTION85.3
2.83-2.910.39691420.37931273X-RAY DIFFRACTION98.4
2.91-2.980.39021430.37271244X-RAY DIFFRACTION98.51
2.98-3.070.39381410.35311276X-RAY DIFFRACTION99.51
3.07-3.170.43281490.34281272X-RAY DIFFRACTION99.58
3.17-3.280.37511390.33621267X-RAY DIFFRACTION99.72
3.28-3.420.32161410.30691304X-RAY DIFFRACTION99.38
3.42-3.570.35441350.28451228X-RAY DIFFRACTION99.85
3.57-3.760.35221440.26711283X-RAY DIFFRACTION99.37
3.76-3.990.27461400.24681267X-RAY DIFFRACTION99.29
3.99-4.30.25231460.21751276X-RAY DIFFRACTION99.93
4.3-4.730.2771360.19671282X-RAY DIFFRACTION100
4.74-5.420.24551400.20891281X-RAY DIFFRACTION99.86
5.42-6.820.29111540.24451290X-RAY DIFFRACTION100
6.82-42.990.24861350.19081257X-RAY DIFFRACTION99.22

+
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