[English] 日本語
Yorodumi
- PDB-26ap: Complex between N-lobe Arc mutant F267/F5Phe and nanobody H11 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 26ap
TitleComplex between N-lobe Arc mutant F267/F5Phe and nanobody H11
Components
  • Activity-regulated cytoskeleton-associated protein
  • Nanobody H11
KeywordsIMMUNE SYSTEM / Antibody-antigen complex / Non-canonical amino acids / Pentafluorophenylalanine
Function / homology
Function and homology information


virus-like capsid / vesicle-mediated intercellular transport / neuronal ribonucleoprotein granule / clathrin-coated vesicle membrane / regulation of long-term synaptic potentiation / dendritic spine morphogenesis / NGF-stimulated transcription / regulation of dendritic spine morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization / regulation of neuronal synaptic plasticity ...virus-like capsid / vesicle-mediated intercellular transport / neuronal ribonucleoprotein granule / clathrin-coated vesicle membrane / regulation of long-term synaptic potentiation / dendritic spine morphogenesis / NGF-stimulated transcription / regulation of dendritic spine morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization / regulation of neuronal synaptic plasticity / mRNA transport / long-term memory / regulation of long-term synaptic depression / acrosomal vesicle / long-term synaptic potentiation / protein homooligomerization / endocytosis / modulation of chemical synaptic transmission / extracellular vesicle / early endosome membrane / cell cortex / dendritic spine / cytoskeleton / postsynaptic membrane / postsynaptic density / membrane raft / mRNA binding / neuronal cell body / glutamatergic synapse / structural molecule activity / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Activity-regulated cytoskeleton-associated protein, N-lobe / 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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Activity-regulated cytoskeleton-associated protein
Similarity search - Component
Biological speciesVicugna pacos (alpaca)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMacri, L.M. / Habel, E. / Huber, T.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP230100079 Australia
Australian Research Council (ARC)DP260100191 Australia
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: Genetically Encoded Pentafluorophenylalanine Enables Quantitative Probing of Local Protein Malleability by 19F NMR.
Authors: Paul, N. / Welegedara, A.P. / Frkic, R.L. / Macri, L. / Thompson, T.R.C. / Baber, J.L. / Habel, E. / Abdelkader, E.H. / Qianzhu, H. / Chilton, N.F. / Jackson, C.J. / Bax, A. / Huber, T. / Otting, G.
History
DepositionApr 24, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2026Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 19, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Nanobody H11
A: Activity-regulated cytoskeleton-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1805
Polymers23,8612
Non-polymers3183
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-11 kcal/mol
Surface area10680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.838, 48.370, 43.709
Angle α, β, γ (deg.)90.000, 96.570, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Antibody Nanobody H11


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)
#2: Protein Activity-regulated cytoskeleton-associated protein / hArc / Activity-regulated gene 3.1 protein homolog / ARC/ARG3.1 / Arg3.1


Mass: 9782.659 Da / Num. of mol.: 1 / Mutation: F267(PF5)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARC, KIAA0278 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7LC44
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.56 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% PEG 3350, 0.2 M magnesium chloride, 0.1 M TRIS hydrochloride pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX3 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 13, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.5→28.08 Å / Num. obs: 26954 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 14.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Net I/σ(I): 12
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 2645 / CC1/2: 0.745

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→28.08 Å / SU ML: 0.1494 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.1875
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1936 1380 5.12 %
Rwork0.16 25574 -
obs0.1619 26954 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.65 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1608 0 21 239 1868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841831
X-RAY DIFFRACTIONf_angle_d1.02872487
X-RAY DIFFRACTIONf_chiral_restr0.0563239
X-RAY DIFFRACTIONf_plane_restr0.0094328
X-RAY DIFFRACTIONf_dihedral_angle_d15.7846695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.560.25251580.20672487X-RAY DIFFRACTION98.95
1.56-1.620.25541120.1932580X-RAY DIFFRACTION99.89
1.62-1.690.23061110.18512559X-RAY DIFFRACTION99.89
1.69-1.780.1931550.17172517X-RAY DIFFRACTION99.96
1.78-1.890.20741300.17442569X-RAY DIFFRACTION99.93
1.9-2.040.1971390.15562567X-RAY DIFFRACTION100
2.04-2.250.19891130.15122576X-RAY DIFFRACTION99.93
2.25-2.570.17051480.16022558X-RAY DIFFRACTION99.93
2.57-3.240.22531590.16122542X-RAY DIFFRACTION99.96
3.24-28.080.16681550.14482619X-RAY DIFFRACTION99.93

+
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