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- PDB-6bca: A Complex between PH Domain of LbcRhoGEF (AKAP-Lbc) and Activated... -

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Basic information

Entry
Database: PDB / ID: 6bca
TitleA Complex between PH Domain of LbcRhoGEF (AKAP-Lbc) and Activated RhoA Bound to a GTP Analog
Components
  • A-kinase anchor protein 13
  • Transforming protein RhoA
KeywordsSIGNALING PROTEIN / Rho GTPase Guanine Nucleotide Exchange Factors RhoGEF Pleckstrin Homology PH domain
Function / homology
Function and homology information


regulation of sarcomere organization / alpha-beta T cell lineage commitment / aortic valve formation / beta selection / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / bone trabecula morphogenesis / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins ...regulation of sarcomere organization / alpha-beta T cell lineage commitment / aortic valve formation / beta selection / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / bone trabecula morphogenesis / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / cleavage furrow formation / negative regulation of cell size / cardiac muscle cell differentiation / regulation of osteoblast proliferation / regulation of modification of postsynaptic actin cytoskeleton / MAP kinase scaffold activity / mitotic cleavage furrow formation / apical junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / establishment of epithelial cell apical/basal polarity / positive regulation of alpha-beta T cell differentiation / cell junction assembly / cellular response to chemokine / regulation of Rho protein signal transduction / negative regulation of oxidative phosphorylation / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / odontogenesis / regulation of small GTPase mediated signal transduction / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / Sema4D mediated inhibition of cell attachment and migration / wound healing, spreading of cells / stress fiber assembly / Wnt signaling pathway, planar cell polarity pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / regulation of focal adhesion assembly / ossification involved in bone maturation / positive regulation of protein serine/threonine kinase activity / negative chemotaxis / RHOB GTPase cycle / NRAGE signals death through JNK / EPHA-mediated growth cone collapse / adrenergic receptor signaling pathway / apical junction complex / myosin binding / positive regulation of cytokinesis / RHOC GTPase cycle / positive regulation of Rho protein signal transduction / cellular response to cytokine stimulus / ERBB2 Regulates Cell Motility / protein kinase A binding / cleavage furrow / semaphorin-plexin signaling pathway / negative regulation of cell-substrate adhesion / mitotic spindle assembly / Rho protein signal transduction / ficolin-1-rich granule membrane / RHOA GTPase cycle / endothelial cell migration / positive regulation of stress fiber assembly / substrate adhesion-dependent cell spreading / positive regulation of T cell migration / positive regulation of neuron differentiation / RHO GTPases activate PKNs / GPVI-mediated activation cascade / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / EPHB-mediated forward signaling / regulation of cell migration / substantia nigra development / guanyl-nucleotide exchange factor activity / secretory granule membrane / cell periphery / regulation of actin cytoskeleton organization / small monomeric GTPase / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of microtubule cytoskeleton organization / bone development / RHO GTPases Activate Formins / positive regulation of non-canonical NF-kappaB signal transduction / cell junction / VEGFA-VEGFR2 Pathway / small GTPase binding / ruffle membrane / heart development / cytoplasmic side of plasma membrane / actin cytoskeleton organization / Ovarian tumor domain proteases / cell migration / G beta:gamma signalling through PI3Kgamma / lamellipodium
Similarity search - Function
RII binding domain / RII binding domain / : / ARHGEF1-like, PH domain / PH domain / Small GTPase Rho / Small GTPase Rho domain profile. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases ...RII binding domain / RII binding domain / : / ARHGEF1-like, PH domain / PH domain / Small GTPase Rho / Small GTPase Rho domain profile. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / C1-like domain superfamily / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / PH-like domain superfamily / Roll / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Transforming protein RhoA / A-kinase anchor protein 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.995 Å
AuthorsSternweis, P.C. / Chen, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH-5R01GM031954 United States
CitationJournal: Data Brief / Year: 2018
Title: Crystal structures of the PH domains from Lbc family of RhoGEFs bound to activated RhoA GTPase.
Authors: Chen, Z. / Gutowski, S. / Sternweis, P.C.
History
DepositionOct 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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.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.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Transforming protein RhoA
A: A-kinase anchor protein 13
B: A-kinase anchor protein 13
C: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8428
Polymers76,7154
Non-polymers1,1274
Water8,773487
1
F: Transforming protein RhoA
B: A-kinase anchor protein 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9214
Polymers38,3572
Non-polymers5642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-29 kcal/mol
Surface area16130 Å2
MethodPISA
2
A: A-kinase anchor protein 13
C: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9214
Polymers38,3572
Non-polymers5642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-28 kcal/mol
Surface area16110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.346, 60.525, 63.618
Angle α, β, γ (deg.)91.83, 92.97, 90.01
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Transforming protein RhoA / Rho cDNA clone 12 / h12


Mass: 20865.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Plasmid: pGEX-kG-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61586
#2: Protein A-kinase anchor protein 13 / AKAP-13 / AKAP-Lbc / Breast cancer nuclear receptor-binding auxiliary protein / Guanine nucleotide ...AKAP-13 / AKAP-Lbc / Breast cancer nuclear receptor-binding auxiliary protein / Guanine nucleotide exchange factor Lbc / Human thyroid-anchoring protein 31 / Lymphoid blast crisis oncogene / LBC oncogene / Non-oncogenic Rho GTPase-specific GTP exchange factor / Protein kinase A-anchoring protein 13 / PRKA13 / p47


Mass: 17491.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKAP13, BRX, HT31, LBC / Plasmid: pGEX-kG-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12802
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 24-26% PEG 3350, 100mM Bis-Tris, 200mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2012
RadiationMonochromator: silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.995→34.212 Å / Num. obs: 50558 / % possible obs: 97.4 % / Redundancy: 2.5 % / Biso Wilson estimate: 22.8 Å2 / Rsym value: 0.1 / Net I/σ(I): 11
Reflection shellResolution: 1.995→2.03 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2327 / Rsym value: 0.4 / % possible all: 90.7

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.995→34.212 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.26
RfactorNum. reflection% reflection
Rfree0.2338 2500 4.95 %
Rwork0.1963 --
obs0.1982 50522 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 1.995→34.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5091 0 66 487 5644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155260
X-RAY DIFFRACTIONf_angle_d1.5327102
X-RAY DIFFRACTIONf_dihedral_angle_d15.9852038
X-RAY DIFFRACTIONf_chiral_restr0.081790
X-RAY DIFFRACTIONf_plane_restr0.007895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9954-2.03370.34311370.26262367X-RAY DIFFRACTION87
2.0337-2.07520.29681240.24062588X-RAY DIFFRACTION94
2.0752-2.12040.29771300.22912664X-RAY DIFFRACTION96
2.1204-2.16970.27031430.2252636X-RAY DIFFRACTION97
2.1697-2.22390.2581410.20942693X-RAY DIFFRACTION97
2.2239-2.2840.24741450.20262650X-RAY DIFFRACTION97
2.284-2.35120.27091390.20132698X-RAY DIFFRACTION98
2.3512-2.42710.26321520.18642671X-RAY DIFFRACTION98
2.4271-2.51380.22981460.19312652X-RAY DIFFRACTION98
2.5138-2.61450.25641350.18132705X-RAY DIFFRACTION98
2.6145-2.73340.23841400.19022714X-RAY DIFFRACTION98
2.7334-2.87740.2641360.19712702X-RAY DIFFRACTION98
2.8774-3.05760.25421280.20582723X-RAY DIFFRACTION98
3.0576-3.29350.29021390.21172682X-RAY DIFFRACTION98
3.2935-3.62460.21381390.19042715X-RAY DIFFRACTION99
3.6246-4.14830.19651340.17822716X-RAY DIFFRACTION99
4.1483-5.22350.13571380.15932733X-RAY DIFFRACTION99
5.2235-34.21730.23851540.21182713X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 15.1972 Å / Origin y: 46.5359 Å / Origin z: 75.7532 Å
111213212223313233
T0.1191 Å20.0212 Å2-0.0055 Å2-0.1313 Å20.0104 Å2--0.1053 Å2
L0.4121 °20.3736 °20.0783 °2-0.4804 °20.0544 °2--0.0478 °2
S0.0224 Å °-0.0236 Å °-0.0058 Å °0.0094 Å °-0.014 Å °-0.0155 Å °0.0087 Å °0.0037 Å °-0.0035 Å °
Refinement TLS groupSelection details: all

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