[English] 日本語
Yorodumi
- PDB-8ze8: Arf-GTPase activating protein Asap1 SH3 domain in complex with 44... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ze8
TitleArf-GTPase activating protein Asap1 SH3 domain in complex with 440 Kd Ankyrin-B fragment
Components
  • Ankyrin-2
  • Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
KeywordsPROTEIN BINDING / complex
Function / homology
Function and homology information


VxPx cargo-targeting to cilium / protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / : / : / positive regulation of membrane tubulation / positive regulation of potassium ion transmembrane transporter activity / protein localization to M-band / T-tubule organization ...VxPx cargo-targeting to cilium / protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / : / : / positive regulation of membrane tubulation / positive regulation of potassium ion transmembrane transporter activity / protein localization to M-band / T-tubule organization / SA node cell action potential / membrane depolarization during SA node cell action potential / protein localization to organelle / paranodal junction assembly / sarcoplasmic reticulum calcium ion transport / negative regulation of dendritic spine development / regulation of atrial cardiac muscle cell action potential / atrial cardiac muscle cell action potential / phosphorylation-dependent protein binding / positive regulation of cation channel activity / regulation of SA node cell action potential / protein localization to endoplasmic reticulum / cell projection membrane / cytoskeletal anchor activity / atrial septum development / costamere / positive regulation of potassium ion transport / ventricular cardiac muscle cell action potential / response to methylmercury / protein localization to cilium / positive regulation of calcium ion transport / regulation of release of sequestered calcium ion into cytosol / regulation of ventricular cardiac muscle cell membrane repolarization / regulation of cardiac muscle cell contraction / protein localization to cell surface / M band / positive regulation of podosome assembly / regulation of postsynapse organization / A band / Interaction between L1 and Ankyrins / regulation of cardiac muscle contraction by calcium ion signaling / podosome / spectrin binding / phosphatidylserine binding / regulation of heart rate by cardiac conduction / phosphatidylinositol-3,4,5-trisphosphate binding / regulation of calcium ion transport / cilium assembly / intercalated disc / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / COPI-mediated anterograde transport / phosphatidylinositol-4,5-bisphosphate binding / T-tubule / GTPase activator activity / regulation of heart rate / trans-Golgi network membrane / protein localization to plasma membrane / regulation of protein stability / sarcolemma / recycling endosome / SH3 domain binding / structural constituent of cytoskeleton / centriolar satellite / Z disc / intracellular calcium ion homeostasis / endocytosis / intracellular protein localization / protein transport / ATPase binding / protein-macromolecule adaptor activity / basolateral plasma membrane / dendritic spine / transmembrane transporter binding / postsynaptic membrane / cytoskeleton / early endosome / lysosome / neuron projection / protein stabilization / apical plasma membrane / Golgi membrane / positive regulation of gene expression / protein kinase binding / glutamatergic synapse / enzyme binding / mitochondrion / zinc ion binding / plasma membrane / cytosol
Similarity search - Function
ASAP1, BAR domain / ASAP1, SH3 domain / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / BAR domain of APPL family / Ankyrin, UPA domain / UPA domain / : / Arf GTPase activating protein / ArfGAP domain superfamily ...ASAP1, BAR domain / ASAP1, SH3 domain / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / BAR domain of APPL family / Ankyrin, UPA domain / UPA domain / : / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / BAR domain / Ankyrin repeats (many copies) / AH/BAR domain superfamily / Death domain profile. / Variant SH3 domain / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / PH domain / Death-like domain superfamily / Ankyrin repeat / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily
Similarity search - Domain/homology
Ankyrin-2 / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsChen, K. / Li, Y. / Zhao, Y. / He, Y. / Zhang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Arf GTPase-activating protein ASAP1 specifically binds to 440-kD ankyrin-B
Authors: Li, Y. / Zhao, Y. / He, Y. / Liu, F. / Xia, L. / Liu, K. / Chen, K. / Zhang, M.
History
DepositionMay 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
E: Ankyrin-2
B: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
C: Ankyrin-2
D: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
F: Ankyrin-2
G: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
H: Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1029
Polymers37,0108
Non-polymers921
Water5,585310
1
A: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
E: Ankyrin-2


Theoretical massNumber of molelcules
Total (without water)9,2522
Polymers9,2522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-1 kcal/mol
Surface area4330 Å2
MethodPISA
2
B: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
C: Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3453
Polymers9,2522
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-1 kcal/mol
Surface area4520 Å2
MethodPISA
3
D: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
F: Ankyrin-2


Theoretical massNumber of molelcules
Total (without water)9,2522
Polymers9,2522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-2 kcal/mol
Surface area4290 Å2
MethodPISA
4
G: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
H: Ankyrin-2


Theoretical massNumber of molelcules
Total (without water)9,2522
Polymers9,2522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-1 kcal/mol
Surface area4260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.922, 52.074, 56.909
Angle α, β, γ (deg.)111.42, 90.16, 112.46
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1 / 130 kDa phosphatidylinositol 4 / 5-bisphosphate-dependent ARF1 GTPase-activating protein / ADP- ...130 kDa phosphatidylinositol 4 / 5-bisphosphate-dependent ARF1 GTPase-activating protein / ADP-ribosylation factor-directed GTPase-activating protein 1 / ARF GTPase-activating protein 1 / Development and differentiation-enhancing factor 1 / DEF-1 / Differentiation-enhancing factor 1 / PIP2-dependent ARF1 GAP


Mass: 7794.611 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Asap1, Ddef1, Kiaa1249, Shag1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QWY8
#2: Protein/peptide
Ankyrin-2 / ANK-2 / Ankyrin-B / Brain ankyrin / Non-erythroid ankyrin


Mass: 1457.849 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q01484
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES monohydrate, pH=6.0, 20 % w/v Polyethylene glycol 6,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.07→32.49 Å / Num. obs: 23173 / % possible obs: 97.6 % / Redundancy: 3.2 % / CC1/2: 0.941 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.08 / Rrim(I) all: 0.146 / Χ2: 0.77 / Net I/σ(I): 8.1 / Num. measured all: 75254
Reflection shellResolution: 2.07→2.12 Å / % possible obs: 95.4 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.213 / Num. measured all: 4758 / Num. unique obs: 1695 / CC1/2: 0.674 / Rpim(I) all: 0.153 / Rrim(I) all: 0.264 / Χ2: 0.7 / Net I/σ(I) obs: 5.7

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
Cootmodel building
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JV3

3jv3


Resolution: 2.07→32.4 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 1131 4.89 %
Rwork0.1838 --
obs0.1859 23128 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→32.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 0 6 310 2547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132280
X-RAY DIFFRACTIONf_angle_d1.2843079
X-RAY DIFFRACTIONf_dihedral_angle_d6.45291
X-RAY DIFFRACTIONf_chiral_restr0.066337
X-RAY DIFFRACTIONf_plane_restr0.013398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.160.2711270.19882716X-RAY DIFFRACTION96
2.16-2.280.24411640.19682721X-RAY DIFFRACTION96
2.28-2.420.24591300.18372697X-RAY DIFFRACTION97
2.42-2.610.2291460.19462776X-RAY DIFFRACTION97
2.61-2.870.24591480.18652740X-RAY DIFFRACTION98
2.87-3.290.25851230.1832773X-RAY DIFFRACTION98
3.29-4.140.17251470.16252787X-RAY DIFFRACTION99
4.14-32.40.21131460.1892787X-RAY DIFFRACTION99

+
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