[English] 日本語
Yorodumi
- PDB-3rcp: Crystal structure of the FAPP1 pleckstrin homology domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rcp
TitleCrystal structure of the FAPP1 pleckstrin homology domain
ComponentsPleckstrin homology domain-containing family A member 3
KeywordsMEMBRANE PROTEIN / FAPP1 / PH domain / Lipid-binding / Membrane / seven-stranded-barrel capped by an helix at one edge / phospholipid Binding
Function / homology
Function and homology information


receptor recycling / endosome organization / retrograde transport, endosome to Golgi / phosphatidylinositol-4-phosphate binding / Synthesis of PIPs at the plasma membrane / trans-Golgi network / recycling endosome / early endosome / Golgi membrane / Golgi apparatus ...receptor recycling / endosome organization / retrograde transport, endosome to Golgi / phosphatidylinositol-4-phosphate binding / Synthesis of PIPs at the plasma membrane / trans-Golgi network / recycling endosome / early endosome / Golgi membrane / Golgi apparatus / identical protein binding / cytosol
Similarity search - Function
PH domain containing protein Boi1/Boi2-like / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Pleckstrin homology domain-containing family A member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsRoy, S. / He, J. / Kutateladze, T.G.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Molecular Basis of Phosphatidylinositol 4-Phosphate and ARF1 GTPase Recognition by the FAPP1 Pleckstrin Homology (PH) Domain.
Authors: He, J. / Scott, J.L. / Heroux, A. / Roy, S. / Lenoir, M. / Overduin, M. / Stahelin, R.V. / Kutateladze, T.G.
History
DepositionMar 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pleckstrin homology domain-containing family A member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0802
Polymers11,9881
Non-polymers921
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Pleckstrin homology domain-containing family A member 3
hetero molecules

A: Pleckstrin homology domain-containing family A member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1604
Polymers23,9762
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3090 Å2
ΔGint-9 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.025, 31.025, 216.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Pleckstrin homology domain-containing family A member 3 / PH domain-containing family A member 3 / Phosphatidylinositol-four-phosphate adapter protein 1 / ...PH domain-containing family A member 3 / Phosphatidylinositol-four-phosphate adapter protein 1 / FAPP-1 / Phosphoinositol 4-phosphate adapter protein 1


Mass: 11988.104 Da / Num. of mol.: 1 / Fragment: Residues 1-99, PH domain / Mutation: C94S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAPP1, PLEKHA3 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q9HB20
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: precipitant solution containing 0.1 M NaAc, pH 4.6, 50mM (NH4)2SO4 and 15% PEG1000., VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 5, 2010 / Details: mirrors
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30.7118 Å / Num. all: 15767 / Num. obs: 15364 / % possible obs: 96.42 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 35.2 Å2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 6.7 / Num. unique all: 455 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
HKL2Mapmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
d*TREKdata reduction
d*TREKdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→29.826 Å / SU ML: 0.24 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 1513 9.85 %Random
Rwork0.2302 ---
all0.265 15767 --
obs0.2328 15364 96.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.281 Å2 / ksol: 0.421 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.1745 Å2-0 Å20 Å2
2---4.1745 Å2-0 Å2
3---8.349 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms806 0 6 65 877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017829
X-RAY DIFFRACTIONf_angle_d1.5731117
X-RAY DIFFRACTIONf_dihedral_angle_d17.89304
X-RAY DIFFRACTIONf_chiral_restr0.113119
X-RAY DIFFRACTIONf_plane_restr0.01138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9003-1.96170.3041350.27261207X-RAY DIFFRACTION92
1.9617-2.03180.26461340.26231188X-RAY DIFFRACTION91
2.0318-2.11310.30731370.24811210X-RAY DIFFRACTION94
2.1131-2.20920.23731370.2311276X-RAY DIFFRACTION95
2.2092-2.32570.28311300.23191239X-RAY DIFFRACTION96
2.3257-2.47130.3361390.24841264X-RAY DIFFRACTION98
2.4713-2.6620.28291300.24611297X-RAY DIFFRACTION98
2.662-2.92970.25451370.2311280X-RAY DIFFRACTION98
2.9297-3.35310.22241460.21471298X-RAY DIFFRACTION99
3.3531-4.22270.21771430.20041290X-RAY DIFFRACTION100
4.2227-29.82990.25151450.23231302X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 1.1866 Å / Origin y: 11.0703 Å / Origin z: 15.0538 Å
111213212223313233
T0.0989 Å2-0.0008 Å20.0586 Å2-0.1238 Å20.0022 Å2--0.1415 Å2
L0.8327 °2-0.3922 °20.3915 °2-0.2563 °2-0.0948 °2--0.3015 °2
S0.0312 Å °-0.1805 Å °-0.1962 Å °0.0401 Å °0.0787 Å °0.1756 Å °-0.0067 Å °-0.0718 Å °0.3386 Å °
Refinement TLS groupSelection details: chain A

+
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://pdbjlvh1.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