[English] 日本語
Yorodumi
- PDB-4f1p: Crystal Structure of mutant S554D for ArfGAP and ANK repeat domai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f1p
TitleCrystal Structure of mutant S554D for ArfGAP and ANK repeat domain of ACAP1
ComponentsArf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
KeywordsPROTEIN TRANSPORT / ArfGAP domain / ANK repeat / zinc-binding module
Function / homology
Function and homology information


GTPase activator activity / recycling endosome membrane / protein transport / membrane / metal ion binding
Similarity search - Function
ArfGAP ACAP1/2/3-like / Arf GTPase activating protein / BAR domain of APPL family / 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 / BAR domain ...ArfGAP ACAP1/2/3-like / Arf GTPase activating protein / BAR domain of APPL family / 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 / BAR domain / Annexin V; domain 1 / AH/BAR domain superfamily / Ankyrin repeat-containing domain / PH domain / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily / Alpha Horseshoe / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSun, F. / Pang, X. / Zhang, K. / Ma, J. / Zhou, Q.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Mechanistic insights into regulated cargo binding by ACAP1 protein
Authors: Bai, M. / Pang, X. / Lou, J. / Zhou, Q. / Zhang, K. / Ma, J. / Li, J. / Sun, F. / Hsu, V.W.
History
DepositionMay 7, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
B: Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7006
Polymers78,3772
Non-polymers3234
Water2,126118
1
A: Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3503
Polymers39,1881
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3503
Polymers39,1881
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.561, 163.460, 41.184
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1 / Centaurin-beta-1 / Cnt-b1


Mass: 39188.473 Da / Num. of mol.: 2
Fragment: ArfGAP and ANK repeat domains, UNP residues 378-740
Mutation: S554D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACAP1, CENTB1, KIAA0050 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15027
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 0.2M ammonium sulfate, 12-14% PEG 3350, 0.1M Sodium Citrate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.2 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 19, 2008
RadiationMonochromator: Numerical link type Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 33326 / Num. obs: 32470 / % possible obs: 97.4 % / Observed criterion σ(I): -0.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.393 / % possible all: 91.9

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.412 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23496 1635 5 %RANDOM
Rwork0.21714 ---
obs0.21807 30786 97.45 %-
all-31604 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.388 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---2.62 Å20 Å2
3---3.25 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3706 0 12 118 3836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193811
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0931.9635181
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9675496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.7824.545154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9915633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1791522
X-RAY DIFFRACTIONr_chiral_restr0.0710.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212856
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.21790
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2910.22611
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2150
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2881.52553
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.48823953
X-RAY DIFFRACTIONr_scbond_it0.9631422
X-RAY DIFFRACTIONr_scangle_it1.5144.51228
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 95 -
Rwork0.284 1909 -
obs--91.22 %
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)
14.6079-0.42570.96674.0696-1.06733.48320.13730.0171-0.13890.3802-0.0102-0.2013-0.3460.0841-0.1270.1374-0.0320.00130.0154-0.01140.027232.405735.74165.7174
27.413-0.0947-1.54664.2655-0.0852.49590.14660.40360.3255-0.09640.05210.4414-0.0672-0.1948-0.19870.06840.00970.01910.07220.0530.08617.681749.7901-14.8788
35.41572.91591.88742.50081.18212.44170.06260.1988-0.33390.0720.0633-0.08220.0326-0.0383-0.12590.06860.00280.01310.0503-0.07670.142519.871714.2644-5.4666
45.21621.5372-1.48012.363-1.07521.89120.05920.14370.36530.09180.09650.20680.0256-0.0561-0.15570.10150.03210.02160.06030.09820.177132.330169.9925-25.53
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A407 - 524
2X-RAY DIFFRACTION2B407 - 524
3X-RAY DIFFRACTION3A569 - 697
4X-RAY DIFFRACTION4B569 - 697

+
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