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- PDB-4itr: Crystal Structure of IbpAFic2-H3717A in complex with adenylylated... -

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Basic information

Entry
Database: PDB / ID: 4itr
TitleCrystal Structure of IbpAFic2-H3717A in complex with adenylylated Cdc42
Components
  • Adenosine monophosphate-protein transferase and cysteine protease IbpA
  • Cell division control protein 42 homolog
KeywordsTRANSFERASE / Fic domain / Adenosine monophosphate-protein transferase
Function / homology
Function and homology information


GBD domain binding / submandibular salivary gland formation / Golgi transport complex / positive regulation of pinocytosis / AMPylase activity / actin filament branching / protein adenylylation / positive regulation of synapse structural plasticity / protein adenylyltransferase / dendritic cell migration ...GBD domain binding / submandibular salivary gland formation / Golgi transport complex / positive regulation of pinocytosis / AMPylase activity / actin filament branching / protein adenylylation / positive regulation of synapse structural plasticity / protein adenylyltransferase / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / organelle transport along microtubule / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / GTP-dependent protein binding / Inactivation of CDC42 and RAC1 / cardiac conduction system development / modulation by host of viral process / establishment of Golgi localization / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / mitogen-activated protein kinase kinase kinase binding / thioesterase binding / regulation of modification of postsynaptic structure / regulation of stress fiber assembly / regulation of lamellipodium assembly / adherens junction organization / embryonic heart tube development / RHO GTPases activate KTN1 / DCC mediated attractive signaling / regulation of postsynapse organization / CD28 dependent Vav1 pathway / negative regulation of GTPase activity / sprouting angiogenesis / positive regulation of filopodium assembly / Wnt signaling pathway, planar cell polarity pathway / nuclear migration / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / small GTPase-mediated signal transduction / Myogenesis / heart contraction / establishment of cell polarity / establishment or maintenance of cell polarity / Golgi organization / RHOJ GTPase cycle / positive regulation of cytokinesis / RHOQ GTPase cycle / RHO GTPases activate PAKs / RHOU GTPase cycle / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / spindle midzone / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / GPVI-mediated activation cascade / phagocytic vesicle / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / RAC1 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / secretory granule / small monomeric GTPase / actin filament organization / positive regulation of DNA replication / integrin-mediated signaling pathway / filopodium / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / cell outer membrane / positive regulation of JNK cascade / RHO GTPases Activate Formins / EGFR downregulation / MAPK6/MAPK4 signaling / protein modification process / Schaffer collateral - CA1 synapse / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / G beta:gamma signalling through CDC42
Similarity search - Function
Peptidase C58, Yersinia/Haemophilus virulence surface antigen / Yersinia/Haemophilus virulence surface antigen / Peptidase C58, YopT-type domain / Fido domain-containing protein / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / ESPR domain ...Peptidase C58, Yersinia/Haemophilus virulence surface antigen / Yersinia/Haemophilus virulence surface antigen / Peptidase C58, YopT-type domain / Fido domain-containing protein / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / ESPR domain / Extended Signal Peptide of Type V secretion system / Cdc42 / Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Small GTPase Rho / small GTPase Rho family profile. / Pectin lyase fold / Pectin lyase fold/virulence factor / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Papain-like cysteine peptidase superfamily / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / Cell division control protein 42 homolog / Protein adenylyltransferase and cysteine protease IbpA
Similarity search - Component
Biological speciesHaemophilus somnus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXiao, J. / Dixon, J.E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural basis of Fic-mediated adenylylation.
Authors: Xiao, J. / Worby, C.A. / Mattoo, S. / Sankaran, B. / Dixon, J.E.
History
DepositionJan 18, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 20, 2013ID: 3N3V
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 2.0Jun 7, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.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_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Revision 3.0Apr 23, 2025Group: Atomic model / Category: atom_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosine monophosphate-protein transferase and cysteine protease IbpA
B: Adenosine monophosphate-protein transferase and cysteine protease IbpA
C: Cell division control protein 42 homolog
D: Cell division control protein 42 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,56914
Polymers113,5554
Non-polymers2,01410
Water14,934829
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint-149 kcal/mol
Surface area41970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.495, 90.997, 190.969
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Adenosine monophosphate-protein transferase and cysteine protease IbpA / HMW IgBP / p120 / Adenosine monophosphate-protein transferase IbpA / AMPylator IbpA / Cysteine ...HMW IgBP / p120 / Adenosine monophosphate-protein transferase IbpA / AMPylator IbpA / Cysteine protease IbpA / Protein p76 IgBP / 76 kDa antigen


Mass: 35493.902 Da / Num. of mol.: 2 / Fragment: Fido 2 domain (UNP residues 3482-3797) / Mutation: H3717A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus somnus (bacteria) / Strain: 2336 / Gene: ibpA, p76, HSM_1489 / Production host: Escherichia coli (E. coli)
References: UniProt: Q06277, nicotinamide-nucleotide adenylyltransferase
#2: Protein Cell division control protein 42 homolog / G25K GTP-binding protein


Mass: 21283.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Production host: Escherichia coli (E. coli) / References: UniProt: P60953

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Non-polymers , 5 types, 839 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 829 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 3350, Bis-Tris, (NH4)2SO4, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2009
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 49917 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.117
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2 / Num. unique all: 4766 / % possible all: 97.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→44.955 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 21.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 2524 5.07 %random
Rwork0.1781 ---
obs0.1806 49826 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→44.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7431 0 124 829 8384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047684
X-RAY DIFFRACTIONf_angle_d0.85610422
X-RAY DIFFRACTIONf_dihedral_angle_d15.3792922
X-RAY DIFFRACTIONf_chiral_restr0.0581212
X-RAY DIFFRACTIONf_plane_restr0.0041329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3003-2.34450.27711370.22442444X-RAY DIFFRACTION94
2.3445-2.39240.27411430.20922564X-RAY DIFFRACTION99
2.3924-2.44440.26071440.19812597X-RAY DIFFRACTION100
2.4444-2.50130.25431230.19522573X-RAY DIFFRACTION100
2.5013-2.56380.27421510.19982624X-RAY DIFFRACTION100
2.5638-2.63310.24491310.19572620X-RAY DIFFRACTION100
2.6331-2.71060.25241430.19082601X-RAY DIFFRACTION100
2.7106-2.79810.23791350.19362613X-RAY DIFFRACTION100
2.7981-2.89810.29131490.19232616X-RAY DIFFRACTION100
2.8981-3.01410.24071410.19382625X-RAY DIFFRACTION100
3.0141-3.15120.24661460.19252619X-RAY DIFFRACTION100
3.1512-3.31730.2631260.17842622X-RAY DIFFRACTION100
3.3173-3.52510.22281420.1752661X-RAY DIFFRACTION100
3.5251-3.79710.21981350.16672648X-RAY DIFFRACTION100
3.7971-4.1790.17761380.14962660X-RAY DIFFRACTION100
4.179-4.78310.16841300.14122699X-RAY DIFFRACTION100
4.7831-6.02390.20251460.17492701X-RAY DIFFRACTION100
6.0239-44.96320.18891640.17542815X-RAY DIFFRACTION99

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