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- PDB-3t9k: Crystal Structure of ACAP1 C-portion mutant S554D fused with inte... -

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Basic information

Entry
Database: PDB / ID: 3t9k
TitleCrystal Structure of ACAP1 C-portion mutant S554D fused with integrin beta1 peptide
ComponentsArf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1,Peptide from Integrin beta-1
KeywordsPROTEIN TRANSPORT / ArfGAP domain / ANK repeat / zinc-binding module
Function / homology
Function and homology information


integrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / myoblast fate specification / positive regulation of glutamate uptake involved in transmission of nerve impulse / regulation of inward rectifier potassium channel activity / regulation of collagen catabolic process ...integrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / myoblast fate specification / positive regulation of glutamate uptake involved in transmission of nerve impulse / regulation of inward rectifier potassium channel activity / regulation of collagen catabolic process / integrin alpha9-beta1 complex / cell-cell adhesion mediated by integrin / integrin alpha4-beta1 complex / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / regulation of synapse pruning / formation of radial glial scaffolds / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / reactive gliosis / cerebellar climbing fiber to Purkinje cell synapse / Other semaphorin interactions / CD40 signaling pathway / positive regulation of vascular endothelial growth factor signaling pathway / calcium-independent cell-matrix adhesion / integrin alphav-beta1 complex / positive regulation of fibroblast growth factor receptor signaling pathway / Fibronectin matrix formation / basement membrane organization / myelin sheath abaxonal region / CHL1 interactions / cardiac muscle cell myoblast differentiation / Laminin interactions / germ cell migration / MET interacts with TNS proteins / leukocyte tethering or rolling / cardiac muscle cell differentiation / cell projection organization / Platelet Adhesion to exposed collagen / myoblast fusion / Elastic fibre formation / mesodermal cell differentiation / axon extension / positive regulation of fibroblast migration / cell migration involved in sprouting angiogenesis / wound healing, spreading of epidermal cells / regulation of spontaneous synaptic transmission / heterotypic cell-cell adhesion / myoblast differentiation / integrin complex / dendrite morphogenesis / Basigin interactions / muscle organ development / Molecules associated with elastic fibres / sarcomere organization / lamellipodium assembly / cell adhesion mediated by integrin / negative regulation of Rho protein signal transduction / MET activates PTK2 signaling / maintenance of blood-brain barrier / Syndecan interactions / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / positive regulation of neuroblast proliferation / positive regulation of wound healing / cell-substrate adhesion / homophilic cell adhesion via plasma membrane adhesion molecules / TGF-beta receptor signaling activates SMADs / establishment of mitotic spindle orientation / glial cell projection / cleavage furrow / cellular response to low-density lipoprotein particle stimulus / fibronectin binding / neuroblast proliferation / RHOG GTPase cycle / negative regulation of anoikis / negative regulation of neuron differentiation / ECM proteoglycans / intercalated disc / RAC3 GTPase cycle / RAC2 GTPase cycle / laminin binding / Integrin cell surface interactions / cellular defense response / coreceptor activity / phagocytosis / ruffle / RAC1 GTPase cycle / protein tyrosine kinase binding / cell adhesion molecule binding / GTPase activator activity / cell-matrix adhesion / B cell differentiation / filopodium / synaptic membrane / Signal transduction by L1 / integrin-mediated signaling pathway / RHO GTPases Activate Formins
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 / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Annexin V; domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / EGF-like domain, extracellular / EGF-like domain / AH/BAR domain superfamily / Integrin domain superfamily / Ankyrin repeat-containing domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / PH domain / von Willebrand factor A-like domain superfamily / PH domain profile. / Pleckstrin homology domain. / EGF-like domain signature 1. / 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
Integrin beta-1 / 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
DepositionAug 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,5276
Polymers83,2042
Non-polymers3234
Water3,153175
1
A: Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1,Peptide from Integrin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7633
Polymers41,6021
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1,Peptide from Integrin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7633
Polymers41,6021
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.258, 164.871, 41.665
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 Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1,Peptide from Integrin beta-1 / Centaurin-beta-1 / Cnt-b1 / Fibronectin receptor subunit beta / Glycoprotein IIa / GPIIA / VLA-4 subunit beta


Mass: 41601.969 Da / Num. of mol.: 2 / Mutation: S554D
Source method: isolated from a genetically manipulated source
Details: Fusion protein of ACAP1 C-portion mutant S554D (UNP residues 378-740 from Q15027), LINKER (GSSNSGSNSG), peptide from integrin beta-1 (UNP residues 758-769 from P05556)
Source: (gene. exp.) Homo sapiens (human) / Gene: ACAP1, CENTB1, KIAA0050, ITGB1, FNRB, MDF2, MSK12 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15027, UniProt: P05556
#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 / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2M ammonium sulfate, 14% PEG 3350, 0.1M Sodium Citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 18, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 38344 / Num. obs: 37309 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.41 / % possible all: 83.8

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Processing

Software
NameVersionClassification
MAR345data collection
PHASESphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3jue

3jue


Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 12.967 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 1710 5.1 %RANDOM
Rwork0.18866 ---
all0.19056 32447 --
obs0.19056 31931 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.692 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å20 Å2
2---2.3 Å20 Å2
3---3.47 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4114 0 12 175 4301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214196
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.9565694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5575548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.07524.457175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.00815677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4311526
X-RAY DIFFRACTIONr_chiral_restr0.0930.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213166
X-RAY DIFFRACTIONr_mcbond_it0.5411.52745
X-RAY DIFFRACTIONr_mcangle_it1.03724353
X-RAY DIFFRACTIONr_scbond_it1.78431451
X-RAY DIFFRACTIONr_scangle_it2.914.51341
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 102 -
Rwork0.219 2044 -
obs--87.45 %
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)
16.9961-0.2387-0.79056.5859-1.47323.8050.25580.02780.3719-0.9231-0.1862-0.27790.41590.2231-0.06960.27120.08560.01640.0628-0.01330.040832.0099-35.7193-26.4029
28.0097-4.6705-2.89514.26021.86234.3097-0.1621-0.26120.05410.10350.12720.16040.1852-0.25060.03490.1249-0.0071-0.01010.0925-0.06460.119517.4559-16.2831-14.4295
37.1715-1.03781.76588.2683-2.22024.0250.0661-0.3484-0.32410.03810.25420.87680.0997-0.2541-0.32030.0761-0.012-0.04390.10490.07810.144317.8685-50.2718-5.3813
48.0223-3.21162.85024.2522-1.08333.9270.0034-0.211-0.2189-0.01540.18310.1857-0.12530.0343-0.18640.1328-0.0077-0.0160.08750.10980.163333.9115-69.19835.4511
50.6251-0.41720.131.9762-0.89850.42790.0625-0.0973-0.0029-0.1671-0.0050.02690.09240.0078-0.05750.2630.0269-0.05970.2698-0.05050.166626.942-39.9235-13.1658
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A405 - 528
2X-RAY DIFFRACTION1A999
3X-RAY DIFFRACTION2A568 - 725
4X-RAY DIFFRACTION2A201
5X-RAY DIFFRACTION3B405 - 525
6X-RAY DIFFRACTION3B999
7X-RAY DIFFRACTION4B567 - 721
8X-RAY DIFFRACTION4B202
9X-RAY DIFFRACTION5A1 - 175
10X-RAY DIFFRACTION5B3 - 172

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