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- PDB-3jue: Crystal Structure of ArfGAP and ANK repeat domain of ACAP1 -

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Basic information

Entry
Database: PDB / ID: 3jue
TitleCrystal Structure of ArfGAP and ANK repeat domain of ACAP1
ComponentsARFGAP with coiled-coil, ANK repeat and PH domain-containing protein 1
KeywordsPROTEIN TRANSPORT/ENDOCYTOSIS / ArfGAP domain / ANK repeat / zinc-binding module / GTPase activation / Metal-binding / Nitration / Phosphoprotein / Protein transport / Transport / Zinc-finger / PROTEIN TRANSPORT-ENDOCYTOSIS COMPLEX
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 / BAR domain / ARFGAP/RecO-like zinc finger ...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 / BAR domain / ARFGAP/RecO-like zinc finger / 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 / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / 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 / SAD / Resolution: 2.3 Å
AuthorsPang, X. / Zhang, K. / Ma, J. / Zhou, Q. / Sun, F.
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
DepositionSep 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 16, 2013Group: Database references / Refinement description
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,7407
Polymers78,3212
Non-polymers4195
Water2,396133
1
A: ARFGAP with coiled-coil, ANK repeat and PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4184
Polymers39,1601
Non-polymers2583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ARFGAP with coiled-coil, ANK repeat and PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3223
Polymers39,1601
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.809, 163.473, 41.092
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 39160.461 Da / Num. of mol.: 2 / Fragment: ArfGAP and ANK repeat domain, residues 378-740
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 / 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.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 0.2M ammonium sulfate, 14% PEG 3350, 0.1M Sodium Citrate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.28 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 10, 2008
RadiationMonochromator: Numerical link type Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2.2→48.63 Å / Num. all: 38024 / Num. obs: 36997 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 19.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 1.58 / Num. unique all: 3765 / % possible all: 81.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→45 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.765 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21936 1652 5 %RANDOM
Rwork0.20239 ---
all0.20321 33244 --
obs0.20321 31334 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.46 Å2 / Biso mean: 38.467 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å20 Å2
2---1.24 Å20 Å2
3---2.83 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3782 0 17 133 3932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213900
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.9625303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3725508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.85824.465159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13315645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9371523
X-RAY DIFFRACTIONr_chiral_restr0.0870.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212929
X-RAY DIFFRACTIONr_mcbond_it0.5231.52526
X-RAY DIFFRACTIONr_mcangle_it1.02624039
X-RAY DIFFRACTIONr_scbond_it1.75931374
X-RAY DIFFRACTIONr_scangle_it2.9224.51264
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 105 -
Rwork0.261 2141 -
all-2246 -
obs-2141 94.25 %
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)
14.7834-0.85331.35264.6235-0.52083.90350.0272-0.0395-0.03960.26660.094-0.1764-0.2897-0.0306-0.12110.0872-0.00960.00330.0073-0.00440.012632.243-46.0946.105
24.03592.14881.44312.36350.91031.96410.06390.1209-0.25090.04920.0518-0.02680.0391-0.0398-0.11560.0722-0.00980.01720.0503-0.0380.05220.033-67.585-5.291
35.658-0.7913-0.91313.44490.11072.55530.17810.25920.153-0.0283-0.04250.1492-0.0715-0.1044-0.13550.05750.00820.01810.04310.01360.021118.304-32.226-14.435
44.43481.9279-0.96992.4987-0.87741.74260.01090.1690.24510.02760.06980.02130.0825-0.0056-0.08060.10540.03420.01160.06180.04510.044732.842-12.305-25.96
52.33910.1065-0.41043.13161.81741.59910.1939-0.07990.20811.29870.0364-0.09480.9011-0.0169-0.23020.78210.1268-0.0050.4949-0.06570.299626.906-37.887-8.792
60.50790.2389-0.10691.299-0.54080.64060.00130.1076-0.0450.12320.05920.0416-0.0396-0.0933-0.06050.2071-0.00710.02760.206-0.03630.021126.089-41.273-6.766
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A404 - 524
2X-RAY DIFFRACTION1A999
3X-RAY DIFFRACTION2A569 - 697
4X-RAY DIFFRACTION3B404 - 524
5X-RAY DIFFRACTION3B999
6X-RAY DIFFRACTION4B569 - 701
7X-RAY DIFFRACTION5A1133 - 1135
8X-RAY DIFFRACTION5B1134
9X-RAY DIFFRACTION6A1000 - 1131
10X-RAY DIFFRACTION6B1001 - 1132

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