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- PDB-4nsw: Crystal structure of the BAR-PH domain of ACAP1 -

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Basic information

Entry
Database: PDB / ID: 4nsw
TitleCrystal structure of the BAR-PH domain of ACAP1
ComponentsArf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
KeywordsPROTEIN TRANSPORT / COILED-COIL / BAR DOMAIN / PH DOMAIN / GTPASE ACTIVATION / membrane remodeling
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 / 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 / Arfaptin homology (AH) domain/BAR domain / BAR domain / ARFGAP/RecO-like zinc finger ...ArfGAP ACAP1/2/3-like / 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 / Arfaptin homology (AH) domain/BAR domain / BAR domain / ARFGAP/RecO-like zinc finger / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / 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 / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily / Roll / Up-down Bundle / Mainly Beta / 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 / SAD / Resolution: 2.2 Å
AuthorsPang, X. / Zhang, K. / Ma, J. / Zhou, Q. / Sun, F.
CitationJournal: Dev Cell / Year: 2014
Title: A PH domain in ACAP1 possesses key features of the BAR domain in promoting membrane curvature.
Authors: Xiaoyun Pang / Jun Fan / Yan Zhang / Kai Zhang / Bingquan Gao / Jun Ma / Jian Li / Yuchen Deng / Qiangjun Zhou / Edward H Egelman / Victor W Hsu / Fei Sun /
Abstract: The BAR (Bin-Amphiphysin-Rvs) domain undergoes dimerization to produce a curved protein structure, which superimposes onto membrane through electrostatic interactions to sense and impart membrane ...The BAR (Bin-Amphiphysin-Rvs) domain undergoes dimerization to produce a curved protein structure, which superimposes onto membrane through electrostatic interactions to sense and impart membrane curvature. In some cases, a BAR domain also possesses an amphipathic helix that inserts into the membrane to induce curvature. ACAP1 (Arfgap with Coil coil, Ankyrin repeat, and PH domain protein 1) contains a BAR domain. Here, we show that this BAR domain can neither bind membrane nor impart curvature, but instead requires a neighboring PH (Pleckstrin Homology) domain to achieve these functions. Specific residues within the PH domain are responsible for both membrane binding and curvature generation. The BAR domain adjacent to the PH domain instead interacts with the BAR domains of neighboring ACAP1 proteins to enable clustering at the membrane. Thus, we have uncovered the molecular basis for an unexpected and unconventional collaboration between PH and BAR domains in membrane bending.
History
DepositionNov 29, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)86,6692
Polymers86,6692
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11880 Å2
ΔGint-92 kcal/mol
Surface area37050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.460, 59.720, 168.950
Angle α, β, γ (deg.)90.00, 91.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 43334.348 Da / Num. of mol.: 2 / Fragment: UNP residues 1-377
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M AMMONIUM CITRATE, 10% PEG3350, 6.0MM OCTYL BETA-THIOGLUCOPYRANOSIDE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A111
SYNCHROTRONPhoton Factory BL-17A20.9790.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJun 7, 2009
ADSC QUANTUM 2702CCDJun 9, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(111) DOUBLE CRYSTALSINGLE WAVELENGTHMx-ray1
2NUMERICAL LINK TYPE SI(111) DOUBLE CRYSTALSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9791
ReflectionResolution: 2.2→29.85 Å / Num. all: 43164 / Num. obs: 41826 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 40.9 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 21.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 3.96 / % possible all: 95.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
RESOLVEmodel building
OASISmodel building
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
OASISphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→29.85 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 15.9 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.302 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2059 5 %RANDOM
Rwork0.211 ---
all0.214 41114 --
obs0.214 39141 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.373 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å2-2.2 Å2
2--3.62 Å20 Å2
3----2.15 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5839 0 0 146 5985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225935
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9687986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0265728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27923.186295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.492151114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0531566
X-RAY DIFFRACTIONr_chiral_restr0.1020.2884
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214461
X-RAY DIFFRACTIONr_mcbond_it0.671.53630
X-RAY DIFFRACTIONr_mcangle_it1.28425808
X-RAY DIFFRACTIONr_scbond_it2.22732305
X-RAY DIFFRACTIONr_scangle_it3.7284.52178
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 156 -
Rwork0.278 2649 -
obs--89.25 %
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)
17.4414-0.93794.17930.5072-0.34643.10950.0591-0.38990.0035-0.002-0.05320.0088-0.0058-0.1774-0.00590.1129-0.00640.10.09120.01580.0986-15.6157-1.341132.4278
24.717-1.46372.0960.7811-0.65441.5940.0938-0.3448-0.08950.0648-0.0007-0.03490.16780.0325-0.09310.1822-0.01250.05830.15120.03740.130311.0239-8.379246.2037
35.86970.081-0.57614.9024-3.434710.37020.14780.0479-0.1296-0.1963-0.1195-0.03960.7290.4054-0.02830.53580.1038-0.13650.22750.03430.227140.2939-35.972282.2715
42.25891.46550.14779.00112.63974.0609-0.43530.4440.5067-1.46710.02170.6167-0.8487-0.10750.41350.51840.1013-0.16760.2850.02240.3011-46.88662.0681-12.8652
51.4967-0.28350.9680.2283-0.15660.65090.0936-0.00850.0946-0.0411-0.1233-0.03640.1058-0.00150.02970.23390.00890.09630.36880.04680.2676-9.5988-5.670931.8679
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 250
2X-RAY DIFFRACTION2B0 - 250
3X-RAY DIFFRACTION3A251 - 364
4X-RAY DIFFRACTION4B251 - 361
5X-RAY DIFFRACTION5A401 - 479
6X-RAY DIFFRACTION5B401 - 467

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