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- PDB-1r8m: SEC7 DOMAIN OF THE ARF EXCHANGE FACTOR ARNO WITH BREFELDIN A-SENS... -

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Basic information

Entry
Database: PDB / ID: 1r8m
TitleSEC7 DOMAIN OF THE ARF EXCHANGE FACTOR ARNO WITH BREFELDIN A-SENSITIZING MUTATIONS
ComponentsArno
KeywordsExchange Factor
Function / homology
Function and homology information


Intra-Golgi traffic / inositol 1,4,5 trisphosphate binding / regulation of ARF protein signal transduction / bicellular tight junction / guanyl-nucleotide exchange factor activity / adherens junction / endocytosis / growth cone / actin cytoskeleton organization / Golgi membrane ...Intra-Golgi traffic / inositol 1,4,5 trisphosphate binding / regulation of ARF protein signal transduction / bicellular tight junction / guanyl-nucleotide exchange factor activity / adherens junction / endocytosis / growth cone / actin cytoskeleton organization / Golgi membrane / lipid binding / membrane / 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
FORMIC ACID / : / Cytohesin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRenault, L. / Guibert, B. / Cherfils, J.
CitationJournal: Nature / Year: 2003
Title: Structural snapshots of the mechanism and inhibition of a guanine nucleotide exchange factor
Authors: Renault, L. / Guibert, B. / Cherfils, J.
History
DepositionOct 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE The engineered mutations in the Arno structure (F190Y, A191S, S198D, P208M) are Brefeldin ...SEQUENCE The engineered mutations in the Arno structure (F190Y, A191S, S198D, P208M) are Brefeldin A- sensitizing mutations.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Arno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6163
Polymers23,5151
Non-polymers1012
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.429, 95.775, 33.665
Angle α, β, γ (deg.)90.00, 101.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Arno / ARF nucleotide-binding site opener / cytohesin 2 / ARF exchange factor


Mass: 23514.754 Da / Num. of mol.: 1 / Fragment: Sec7 domain / Mutation: F190Y/A191S/S198D/P208M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSCD2, ARNO / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 gold / References: UniProt: Q99418
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 3350, 190mM Sodium Formate, 100mM Hepes, 18mM MnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.1 mMprotein1drop
220 mMTris1reservoirpH8
320 mM1reservoirKCl
42.5 mMbeta-mercaptoethanol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM30A10.979
SYNCHROTRONESRF ID14-320.933
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9331
ReflectionResolution: 1.7→33 Å / Num. obs: 21082 / Redundancy: 4.5 % / Biso Wilson estimate: 17.61 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 18
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 1.76 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 5 / % possible all: 65.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PBV

1pbv


Resolution: 1.7→32.97 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.465 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23136 1083 5.1 %RANDOM
Rwork0.19209 ---
obs0.19414 19998 93.12 %-
all-21082 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.946 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20.59 Å2
2---0.59 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 0 4 119 1716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221624
X-RAY DIFFRACTIONr_bond_other_d0.0030.021475
X-RAY DIFFRACTIONr_angle_refined_deg1.9421.9712182
X-RAY DIFFRACTIONr_angle_other_deg1.09133435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3325195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.110.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021803
X-RAY DIFFRACTIONr_gen_planes_other0.0230.02334
X-RAY DIFFRACTIONr_nbd_refined0.2350.2353
X-RAY DIFFRACTIONr_nbd_other0.240.21638
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0930.2903
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.298
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3650.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3280.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.3061.5976
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.24521563
X-RAY DIFFRACTIONr_scbond_it3.8213648
X-RAY DIFFRACTIONr_scangle_it5.984.5619
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.751 Å / Total num. of bins used: 19 /
RfactorNum. reflection
Rfree0.271 63
Rwork0.23 1254
Refinement TLS params.Method: refined / Origin x: 2.1822 Å / Origin y: -1.4654 Å / Origin z: 13.5916 Å
111213212223313233
T0.0217 Å2-0.0086 Å2-0.0023 Å2-0.0563 Å2-0.021 Å2--0.0456 Å2
L0.3859 °20.1159 °20.1363 °2-1.2374 °20.1843 °2--0.7605 °2
S0.0275 Å °0.0272 Å °0.0395 Å °0.0013 Å °-0.0848 Å °0.0533 Å °0.0106 Å °-0.0721 Å °0.0573 Å °
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 33 Å / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS

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