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- PDB-4dxa: Co-crystal structure of Rap1 in complex with KRIT1 -

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Basic information

Entry
Database: PDB / ID: 4dxa
TitleCo-crystal structure of Rap1 in complex with KRIT1
Components
  • Krev interaction trapped protein 1
  • Ras-related protein Rap-1b
KeywordsPROTEIN BINDING / GTPase / FERM / Protein-protein interaction / GTP binding / Cytoplasmic
Function / homology
Function and homology information


Rap protein signal transduction / modification of postsynaptic structure / GTPase regulator activity / regulation of cell junction assembly / endothelium development / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / integrin activation ...Rap protein signal transduction / modification of postsynaptic structure / GTPase regulator activity / regulation of cell junction assembly / endothelium development / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / integrin activation / Rap1 signalling / negative regulation of endothelial cell migration / establishment of endothelial barrier / regulation of establishment of cell polarity / MET activates RAP1 and RAC1 / azurophil granule membrane / small GTPase-mediated signal transduction / negative regulation of endothelial cell proliferation / p130Cas linkage to MAPK signaling for integrins / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of angiogenesis / negative regulation of endothelial cell apoptotic process / cellular response to cAMP / phosphatidylinositol-4,5-bisphosphate binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / Integrin signaling / negative regulation of angiogenesis / cell redox homeostasis / small monomeric GTPase / G protein activity / establishment of localization in cell / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / GDP binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cell-cell junction / Signaling by BRAF and RAF1 fusions / microtubule binding / angiogenesis / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / cytoskeleton / GTPase activity / glutamatergic synapse / Neutrophil degranulation / protein-containing complex binding / GTP binding / protein-containing complex / extracellular space / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
KRIT, N-terminal NPxY motif-rich region / Krev interaction trapped protein 1, FERM domain C-lobe / KRIT, N-terminal NPxY motif-rich domain superfamily / NUDIX, or N-terminal NPxY motif-rich, region of KRIT / Ras-related protein Rap1 / Ankyrin repeats (many copies) / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein / FERM central domain / FERM/acyl-CoA-binding protein superfamily ...KRIT, N-terminal NPxY motif-rich region / Krev interaction trapped protein 1, FERM domain C-lobe / KRIT, N-terminal NPxY motif-rich domain superfamily / NUDIX, or N-terminal NPxY motif-rich, region of KRIT / Ras-related protein Rap1 / Ankyrin repeats (many copies) / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / Small GTPase, Ras-type / FERM superfamily, second domain / small GTPase Ras family profile. / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Krev interaction trapped protein 1 / Ras-related protein Rap-1b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLi, X. / Zhang, R. / Boggon, T.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Basis for Small G Protein Effector Interaction of Ras-related Protein 1 (Rap1) and Adaptor Protein Krev Interaction Trapped 1 (KRIT1).
Authors: Li, X. / Zhang, R. / Draheim, K.M. / Liu, W. / Calderwood, D.A. / Boggon, T.J.
History
DepositionFeb 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Jul 25, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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.pdbx_dist_value / _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_ref_seq_dif.details / _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: Ras-related protein Rap-1b
B: Krev interaction trapped protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1434
Polymers56,5792
Non-polymers5642
Water5,891327
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.548, 77.970, 59.757
Angle α, β, γ (deg.)90.000, 90.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ras-related protein Rap-1b / GTP-binding protein smg p21B


Mass: 19206.719 Da / Num. of mol.: 1 / Mutation: G12V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: OK/SW-cl.11, RAP1B, Ras-related protein Rap-1b (RAP1B)
Plasmid: modified pET-32 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA / References: UniProt: P61224, small monomeric GTPase
#2: Protein Krev interaction trapped protein 1 / Krev interaction trapped 1 / Cerebral cavernous malformations 1 protein


Mass: 37372.281 Da / Num. of mol.: 1 / Fragment: FERM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CCM1, Krev interaction trapped protein 1 (KRIT1), KRIT1
Plasmid: pGEX 6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00522
#3: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M KNO3, 20% PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2012
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 37653 / Num. obs: 37653 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 28.6 Å2 / Rsym value: 0.083 / Net I/σ(I): 15.4
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.56 / Num. unique all: 3774 / Rsym value: 0.881 / % possible all: 98.1

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.7.3_928refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C1Y

1c1y


Resolution: 1.95→47.425 Å / Occupancy max: 1 / Occupancy min: 0.44 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 1936 5.18 %RANDOM
Rwork0.1961 ---
obs0.1983 37384 96.89 %-
all-37384 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.45 Å2 / ksol: 0.297 e/Å3
Displacement parametersBiso max: 190.39 Å2 / Biso mean: 41.2223 Å2 / Biso min: 18.13 Å2
Baniso -1Baniso -2Baniso -3
1--6.1315 Å2-0 Å27.6899 Å2
2--2.3246 Å2-0 Å2
3---3.8068 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3818 0 33 327 4178
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)
15.4306-0.88492.11257.7895-7.44978.07220.10480.0470.5846-0.4951-0.5781-0.3110.10340.52840.5160.31560.07820.00910.25130.00580.278921.471319.464419.14
21.66181.62680.86342.22321.32128.2493-0.1648-0.2974-0.8874-0.044-0.1047-0.93910.57380.54080.15070.29520.07030.05020.37110.15840.512631.22744.341322.8397
36.8348-1.2426.58844.5186-1.75438.17440.0036-0.33570.4759-0.4043-0.3764-0.04990.0903-0.58140.3870.26620.0110.02680.3368-0.00930.239424.149916.019515.6803
47.50660.517-0.46052.72734.19776.7039-0.698-1.80240.76241.58580.1174-0.76590.15771.24420.59480.5245-0.0095-0.06450.9298-0.0190.415928.37518.853734.2624
52.87411.261-0.59998.0122-1.18534.1790.1581-0.77450.03930.8316-0.25740.3121-0.216-0.1980.09330.2577-0.05580.02810.4215-0.01560.225717.322211.242733.1607
64.47060.6292-1.14897.5032-1.88424.3393-0.1471-0.0937-0.4653-0.0116-0.12290.38820.429-0.260.23930.2216-0.0609-0.01170.2894-0.02250.267614.9493.323825.2872
76.06422.3543-1.05933.34790.95254.63460.1045-0.4948-0.1640.1782-0.1231-0.30070.26850.1711-0.00350.21450.034-0.01890.2790.04560.256147.469817.690621.2528
83.43390.8926-0.78895.57592.64143.74650.0034-0.32830.0143-0.21060.0252-0.0899-0.20210.2182-0.0260.20570.0499-0.0040.2540.04550.167949.346622.592611.9087
96.1954-2.16231.15945.3293-4.7937.7956-0.3306-0.09760.01020.54660.06840.0008-0.3418-0.19670.23210.2645-0.00080.03590.1616-0.02630.217138.643515.14796.2285
106.95230.6030.57582.9120.46574.4122-0.04460.8660.0752-0.2854-0.00790.40650.0047-0.58290.03260.2776-0.0085-0.00960.4027-0.01380.241228.89215.2439-4.7701
113.12250.9774-0.96695.5045-0.01973.4379-0.07650.34970.3904-0.27150.23360.3088-0.2277-0.0815-0.16130.197-0.02340.02250.25010.07440.266350.992326.7383-2.6845
127.61011.51260.43766.63691.2977.48780.2631-0.02320.5262-0.57930.1475-1.0708-0.85781.1428-0.37990.3321-0.07610.14240.3810.00240.507665.28927.3187-1.725
134.38960.1233-0.5596.6298-2.65564.68710.01930.37030.1213-0.5849-0.0468-0.5801-0.00320.4389-0.00890.2433-0.02060.07290.28490.00290.31462.014124.5566-0.6715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 0:10)A0 - 10
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 11:36)A11 - 36
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 37:58)A37 - 58
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 59:74)A59 - 74
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 75:116)A75 - 116
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 117:167)A117 - 167
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 419:486)B419 - 486
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 487:524)B487 - 524
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 525:541)B525 - 541
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 542:629)B542 - 629
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 630:682)B630 - 682
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 683:701)B683 - 701
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 702:729)B702 - 729

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