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- PDB-4a4p: crystal structure of the Sec7 domain from human cytohesin1 -

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Basic information

Entry
Database: PDB / ID: 4a4p
Titlecrystal structure of the Sec7 domain from human cytohesin1
ComponentsCYTOHESIN1
KeywordsSIGNALING PROTEIN / ALL ALPHA / GUANINE-NUCLEOTIDE RELEASING FACTOR
Function / homology
Function and homology information


establishment of epithelial cell polarity / Intra-Golgi traffic / regulation of ARF protein signal transduction / bicellular tight junction / regulation of cell adhesion / vesicle-mediated transport / guanyl-nucleotide exchange factor activity / adherens junction / cytoplasmic side of plasma membrane / Golgi membrane ...establishment of epithelial cell polarity / Intra-Golgi traffic / regulation of ARF protein signal transduction / bicellular tight junction / regulation of cell adhesion / vesicle-mediated transport / guanyl-nucleotide exchange factor activity / adherens junction / cytoplasmic side of plasma membrane / Golgi membrane / lipid binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Arf Nucleotide-binding Site Opener; domain 2 / Arf Nucleotide-binding Site Opener,domain 2 / Annexin V; domain 1 - #20 / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / Annexin V; domain 1 ...Arf Nucleotide-binding Site Opener; domain 2 / Arf Nucleotide-binding Site Opener,domain 2 / Annexin V; domain 1 - #20 / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / Annexin V; domain 1 / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZeeh, J.C. / Thompson, A.W. / Cherfils, J. / Biou, V.
CitationJournal: To be Published
Title: Crystal Structure of the Sec7 Domain from Human Cytohesin1
Authors: Zeeh, J.C. / Thompson, A.W. / Cherfils, J. / Biou, V.
History
DepositionOct 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: CYTOHESIN1
B: CYTOHESIN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8954
Polymers44,7112
Non-polymers1842
Water6,810378
1
A: CYTOHESIN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4482
Polymers22,3551
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYTOHESIN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4482
Polymers22,3551
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.090, 80.280, 51.900
Angle α, β, γ (deg.)90.00, 90.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.88756, 0.15305, -0.43452), (0.14376, -0.98812, -0.05439), (-0.43768, -0.01419, -0.89902)
Vector: 4.26002, -28.44946, 59.97091)

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Components

#1: Protein CYTOHESIN1 / PH\ / SEC7 AND COILED-COIL DOMAIN-CONTAINING PROTEIN 1 / SEC7 HOMOLOG B2-1


Mass: 22355.488 Da / Num. of mol.: 2 / Fragment: SEC7 DOMAIN, RESIDUES 63-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: Q15438
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.14 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 7
Details: PEG 3350 12%, AMMONIUM ACETATE 0.4M. GLYCEROL CRYO-PROTECTANT., pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 13, 2009 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→80.2 Å / Num. obs: 79470 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 26.48 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R8M

1r8m


Resolution: 2→32.03 Å / Cor.coef. Fo:Fc: 0.9435 / Cor.coef. Fo:Fc free: 0.9199 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 1320 5.08 %RANDOM
Rwork0.1737 ---
obs0.1762 25974 --
Displacement parametersBiso mean: 28.94 Å2
Baniso -1Baniso -2Baniso -3
1-3.0632 Å20 Å23.3895 Å2
2--0.2339 Å20 Å2
3----3.2971 Å2
Refine analyzeLuzzati coordinate error obs: 0.203 Å
Refinement stepCycle: LAST / Resolution: 2→32.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3020 0 12 378 3410
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013088HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.994154HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1126SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes104HARMONIC2
X-RAY DIFFRACTIONt_gen_planes432HARMONIC5
X-RAY DIFFRACTIONt_it3088HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion17.83
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion388SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4063SEMIHARMONIC4
LS refinement shellResolution: 2→2.08 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.268 154 5.25 %
Rwork0.1865 2782 -
all0.1908 2936 -

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