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- PDB-4c0a: Arf1(Delta1-17)in complex with BRAG2 Sec7-PH domain -

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Basic information

Entry
Database: PDB / ID: 4c0a
TitleArf1(Delta1-17)in complex with BRAG2 Sec7-PH domain
Components
  • ADP-RIBOSYLATION FACTOR 1ARF1
  • IQ MOTIF AND SEC7 DOMAIN-CONTAINING PROTEIN 1
KeywordsPROTEIN TRANSPORT / ENDOCYTOSIS
Function / homology
Function and homology information


Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / Intra-Golgi traffic / Synthesis of PIPs at the plasma membrane / Golgi Associated Vesicle Biogenesis / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / Lysosome Vesicle Biogenesis / regulation of ARF protein signal transduction / regulation of receptor internalization ...Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / Intra-Golgi traffic / Synthesis of PIPs at the plasma membrane / Golgi Associated Vesicle Biogenesis / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / Lysosome Vesicle Biogenesis / regulation of ARF protein signal transduction / regulation of receptor internalization / MHC class II antigen presentation / regulation of Arp2/3 complex-mediated actin nucleation / positive regulation of keratinocyte migration / dendritic spine development / positive regulation of focal adhesion disassembly / dendritic spine organization / long-term synaptic depression / vesicle-mediated transport / guanyl-nucleotide exchange factor activity / small monomeric GTPase / intracellular protein transport / synaptic vesicle / actin cytoskeleton organization / postsynaptic density / neuron projection / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / lipid binding / GTP binding / nucleolus / Golgi apparatus / membrane / plasma membrane / cytosol
Similarity search - Function
IQ motif and SEC7 domain-containing protein, PH domain / PH domain / 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. ...IQ motif and SEC7 domain-containing protein, PH domain / PH domain / 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 / ADP-ribosylation factor 1-5 / small GTPase Arf family profile. / Annexin V; domain 1 / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / IQ motif profile. / IQ motif, EF-hand binding site / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Pleckstrin homology domain. / Pleckstrin homology domain / Rab subfamily of small GTPases / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE / ADP-ribosylation factor 1 / IQ motif and SEC7 domain-containing protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
BOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsAizel, K. / Biou, V. / Navaza, J. / Duarte, L. / Campanacci, V. / Cherfils, J. / Zeghouf, M.
CitationJournal: PLoS Biol. / Year: 2013
Title: Integrated conformational and lipid-sensing regulation of endosomal ArfGEF BRAG2.
Authors: Aizel, K. / Biou, V. / Navaza, J. / Duarte, L.V. / Campanacci, V. / Cherfils, J. / Zeghouf, M.
History
DepositionAug 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Nov 21, 2018Group: Data collection / Database references / Category: citation / reflns / reflns_shell
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value
Revision 1.3Dec 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

Downloads & links

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Assembly

Deposited unit
A: IQ MOTIF AND SEC7 DOMAIN-CONTAINING PROTEIN 1
B: IQ MOTIF AND SEC7 DOMAIN-CONTAINING PROTEIN 1
C: ADP-RIBOSYLATION FACTOR 1
D: ADP-RIBOSYLATION FACTOR 1
E: IQ MOTIF AND SEC7 DOMAIN-CONTAINING PROTEIN 1
F: IQ MOTIF AND SEC7 DOMAIN-CONTAINING PROTEIN 1
G: ADP-RIBOSYLATION FACTOR 1
H: ADP-RIBOSYLATION FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,02112
Polymers252,9288
Non-polymers2,0934
Water0
1
B: IQ MOTIF AND SEC7 DOMAIN-CONTAINING PROTEIN 1
G: ADP-RIBOSYLATION FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7553
Polymers63,2322
Non-polymers5231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-18.4 kcal/mol
Surface area24910 Å2
MethodPISA
2
A: IQ MOTIF AND SEC7 DOMAIN-CONTAINING PROTEIN 1
H: ADP-RIBOSYLATION FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7553
Polymers63,2322
Non-polymers5231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-21.3 kcal/mol
Surface area24970 Å2
MethodPISA
3
D: ADP-RIBOSYLATION FACTOR 1
E: IQ MOTIF AND SEC7 DOMAIN-CONTAINING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7553
Polymers63,2322
Non-polymers5231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-21 kcal/mol
Surface area25110 Å2
MethodPISA
4
C: ADP-RIBOSYLATION FACTOR 1
F: IQ MOTIF AND SEC7 DOMAIN-CONTAINING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7553
Polymers63,2322
Non-polymers5231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-14.1 kcal/mol
Surface area24590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.980, 65.780, 196.860
Angle α, β, γ (deg.)90.00, 96.13, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
IQ MOTIF AND SEC7 DOMAIN-CONTAINING PROTEIN 1 / ADP-RIBOSYLATION FACTORS GUANINE NUCLEOTIDE-EXCHANGE PROTEIN 100 / ADP-RIBOSYLATION FACTORS GUANINE ...ADP-RIBOSYLATION FACTORS GUANINE NUCLEOTIDE-EXCHANGE PROTEIN 100 / ADP-RIBOSYLATION FACTORS GUANINE NUCLEOTIDE-EXCHANGE PROTEIN 2 / BREFELDIN-RESISTANT ARF-GEF 2 PROTEIN / BRAG2


Mass: 44409.500 Da / Num. of mol.: 4 / Fragment: SEC7 AND PH DOMAIN, RESIDUES 390-763 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q6DN90
#2: Protein
ADP-RIBOSYLATION FACTOR 1 / ARF1 / ARF1


Mass: 18822.455 Da / Num. of mol.: 4 / Fragment: DELTA17 ARF1, RESIDUES 18-181
Source method: isolated from a genetically manipulated source
Details: GDP-3P LIGAND / Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS / References: UniProt: P84080
#3: Chemical
ChemComp-G3D / GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3
Sequence detailsARF1 WAS DELETED FROM ITS 17 FIRST AMINO ACIDS IN THE STRUCTURE ISOFORM 2 AND IN THE STRUCTURE ...ARF1 WAS DELETED FROM ITS 17 FIRST AMINO ACIDS IN THE STRUCTURE ISOFORM 2 AND IN THE STRUCTURE SEQUENCE REMAINS A PART OF THE CLEAVED 6-HISTAG GAMGSGIP

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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: 2.32 Å3/Da / Density % sol: 46.99 % / Description: NONE
Crystal growpH: 6
Details: 0.15 M AMMONIUM SULFATE, 0.1 M MES PH 6 AND 16% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2011 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.3→42.8 Å / Num. obs: 67437 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.24 % / Biso Wilson estimate: 61.36 Å2 / Rmerge(I) obs: 0.03 / Rsym value: 0.201 / Net I/σ(I): 6.8
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 3.16 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 1.94 / Rsym value: 0.735 / % possible all: 95.6

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R8S AND 3QWM

1r8s

3qwm


Resolution: 3.3→42.84 Å / Cor.coef. Fo:Fc: 0.9122 / Cor.coef. Fo:Fc free: 0.867 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.549
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 1757 5 %RANDOM
Rwork0.1988 ---
obs0.2013 35125 99.28 %-
Displacement parametersBiso mean: 69.56 Å2
Baniso -1Baniso -2Baniso -3
1--11.5765 Å20 Å26.0514 Å2
2--1.1759 Å20 Å2
3---10.4006 Å2
Refine analyzeLuzzati coordinate error obs: 0.715 Å
Refinement stepCycle: LAST / Resolution: 3.3→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16794 0 128 0 16922
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0117243HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3223254HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6370SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes495HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2494HARMONIC5
X-RAY DIFFRACTIONt_it17243HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion22.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2171SEMIHARMONIC5
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_contact20192SEMIHARMONIC4
LS refinement shellResolution: 3.3→3.4 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.254 132 5.02 %
Rwork0.2184 2496 -
all0.2203 2628 -
obs--99.28 %
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)
11.1772-1.3937-0.61312.8080.89122.4836-0.0768-0.04650.06360.13940.2202-0.06080.1137-0.1259-0.1433-0.1974-0.0330.0669-0.0858-0.0214-0.151-65.6304-13.0234-79.584
21.28371.3726-0.24364.0736-1.17091.77230.0090.1357-0.0214-0.2457-0.07930.02060.27120.06830.0703-0.02520.0846-0.0349-0.1771-0.0022-0.2916-14.9652-13.7905-21.0681
39.1464-1.74671.86577.04860.29538.0708-0.29520.4641-0.15750.0176-0.10360.098-0.1190.16790.3989-0.341-0.0654-0.0629-0.2537-0.0125-0.178814.4861-28.1776-38.0779
46.78070.82812.35265.7527-1.22865.0991-0.1724-0.40590.4909-0.0143-0.1261-0.0983-0.12950.27140.2985-0.24870.07970.0254-0.0923-0.0383-0.2432-10.4385-30.2623-54.9273
51.2175-1.2543-0.87463.05811.25842.7888-0.0849-0.0084-0.00880.00170.01380.0610.1976-0.03770.071-0.2129-0.0802-0.0105-0.08130.0396-0.1994-22.8974-46.0897-75.4601
60.53790.8383-0.22452.2419-1.07911.91630.0320.0574-0.11110.1809-0.0742-0.26090.00990.12880.0422-0.03170.06620.01-0.11610.0084-0.121229.4824-46.5683-20.7294
77.33250.03081.76147.7117-2.23915.6048-0.48640.66630.3965-0.25960.32450.89650.1505-0.30670.1618-0.2836-0.2692-0.2268-0.18060.2028-0.1988-28.88474.4235-40.0151
812.8822-0.89090.05023.18474.40944.7945-0.067-1.141.15080.19820.6242-1.07350.02060.4215-0.5573-0.55970.2346-0.2794-0.2364-0.28050.411-53.05284.2422-59.8144
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H

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