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- PDB-9qu1: Crystal structure of the human RalGAPA2 N-terminal domain with hu... -

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Basic information

Entry
Database: PDB / ID: 9qu1
TitleCrystal structure of the human RalGAPA2 N-terminal domain with human kappaB-Ras1
Components
  • NF-kappa-B inhibitor-interacting Ras-like protein 1
  • Ral GTPase-activating protein subunit alpha-2
KeywordsSIGNALING PROTEIN / RAL / GTPase / RalGAP / kB-Ras
Function / homology
Function and homology information


Ral protein signal transduction / regulation of exocyst localization / activation of GTPase activity / RIP-mediated NFkB activation via ZBP1 / regulation of tumor necrosis factor-mediated signaling pathway / surfactant homeostasis / GTPase activating protein binding / regulation of small GTPase mediated signal transduction / lung alveolus development / TRAF6 mediated NF-kB activation ...Ral protein signal transduction / regulation of exocyst localization / activation of GTPase activity / RIP-mediated NFkB activation via ZBP1 / regulation of tumor necrosis factor-mediated signaling pathway / surfactant homeostasis / GTPase activating protein binding / regulation of small GTPase mediated signal transduction / lung alveolus development / TRAF6 mediated NF-kB activation / negative regulation of canonical NF-kappaB signal transduction / GTPase activator activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TAK1-dependent IKK and NF-kappa-B activation / regulation of protein localization / protein heterodimerization activity / GTPase activity / GTP binding / endoplasmic reticulum / extracellular space / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
NF-kappa-B inhibitor-interacting Ras-like protein / Ral GTPase-activating protein subunit alpha/beta, N-terminal domain / RALGAPB N-terminal domain / Tuberin/Ral GTPase-activating protein subunit alpha / Rap/Ran-GAP domain / Rap/Ran-GAP superfamily / Rap/ran-GAP / Rap GTPase activating proteins domain profile. / Small GTPase Rab domain profile. / Ras subfamily of RAS small GTPases ...NF-kappa-B inhibitor-interacting Ras-like protein / Ral GTPase-activating protein subunit alpha/beta, N-terminal domain / RALGAPB N-terminal domain / Tuberin/Ral GTPase-activating protein subunit alpha / Rap/Ran-GAP domain / Rap/Ran-GAP superfamily / Rap/ran-GAP / Rap GTPase activating proteins domain profile. / Small GTPase Rab domain profile. / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ral GTPase-activating protein subunit alpha-2 / NF-kappa-B inhibitor-interacting Ras-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsRasche, R. / Kuemmel, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KU2531/6 Germany
CitationJournal: J Biol Chem / Year: 2025
Title: The GTPase κB-Ras is an essential subunit of the RalGAP tumor suppressor complex.
Authors: René Rasche / Lisa Helene Apken / Sonja Titze / Esther Michalke / Rohit Kumar Singh / Andrea Oeckinghaus / Daniel Kümmel /
Abstract: κB-Ras1 and κB-Ras2 are small GTPases with noncanonical features that act as tumor suppressors downstream of Ras. Via interaction with the RalGAP (GTPase-activating protein) complex, they limit ...κB-Ras1 and κB-Ras2 are small GTPases with noncanonical features that act as tumor suppressors downstream of Ras. Via interaction with the RalGAP (GTPase-activating protein) complex, they limit activity of Ral GTPases and restrict anchorage-independent proliferation. We here present the crystal structure of κB-Ras1 in complex with the N-terminal domain of RGα2. The structure suggests a mechanism of intrinsic GTP hydrolysis of κB-Ras1 that relies on a scaffolding function of the GTPase rather than on catalytic residues, which we confirm by mutational analysis. The interaction with RGα2 is nucleotide independent and does not involve κB-Ras1 switch regions, which establishes κB-Ras proteins as a constitutive third subunit of RalGAP complexes. Functional studies demonstrate that κB-Ras proteins are not required for RalGAP catalytic activity in vitro but for functionality in vivo. We propose that κB-Ras may thus act as a regulator of RalGAP localization and thereby control the Ras-Ral signaling pathway.
History
DepositionApr 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ral GTPase-activating protein subunit alpha-2
B: Ral GTPase-activating protein subunit alpha-2
C: NF-kappa-B inhibitor-interacting Ras-like protein 1
F: NF-kappa-B inhibitor-interacting Ras-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,5708
Polymers99,4774
Non-polymers1,0934
Water57632
1
A: Ral GTPase-activating protein subunit alpha-2
C: NF-kappa-B inhibitor-interacting Ras-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2854
Polymers49,7392
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-28 kcal/mol
Surface area19020 Å2
MethodPISA
2
B: Ral GTPase-activating protein subunit alpha-2
F: NF-kappa-B inhibitor-interacting Ras-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2854
Polymers49,7392
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-30 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.564, 63.430, 104.163
Angle α, β, γ (deg.)90.000, 91.263, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Ral GTPase-activating protein subunit alpha-2 / 250 kDa substrate of Akt / AS250 / p220


Mass: 29617.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal His_Sumo tag MGSSHHHHHH SSGLVPRGSH MASMSDSEVN QEAKPEVKPE VKPETHINLK VSDGSSEIFFKIKKTTPLRR LMEAFAKRQG KEMDSLRFLY DGIRIQADQT PEDLDMEDND IIEAHREQIGGS RalGAP alpha2 amino acids 2-255
Source: (gene. exp.) Homo sapiens (human) / Gene: RALGAPA2, C20orf74, KIAA1272 / Plasmid: pET28HS_p220_2-255
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21 / References: UniProt: Q2PPJ7
#2: Protein NF-kappa-B inhibitor-interacting Ras-like protein 1 / I-kappa-B-interacting Ras-like protein 1 / Kappa B-Ras protein 1 / KappaB-Ras1


Mass: 20121.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: kappaB-Ras1 amino acids 1-175 expressed with N-terminal GST tag with Prescission cleavage site. Tag was cleaved
Source: (gene. exp.) Homo sapiens (human) / Gene: NKIRAS1, KBRAS1 / Plasmid: 247_pCDF6p_kBRas1_1-175
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9NYS0
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.77 Å3/Da / Density % sol: 55.7 % / Description: elongated rod shaped crystal
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 17 % PEG 3350 20 % glycerol 0.1 M MgCl2 1 ul protei + 1 ul screening buffer + 1 ul seed seed (1:200)
Temp details: +/- 2 K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.68879 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.68879 Å / Relative weight: 1
ReflectionResolution: 2.716→104.138 Å / Num. obs: 21842 / % possible obs: 91.5 % / Redundancy: 5.56 % / Biso Wilson estimate: 65.48 Å2 / CC1/2: 0.997 / CC star: 0.99 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.052 / Rrim(I) all: 0.125 / Net I/σ(I): 10.2
Reflection shellResolution: 2.716→2.959 Å / Redundancy: 4.56 % / Rmerge(I) obs: 1.202 / Num. unique obs: 1093 / CC1/2: 0.508 / CC star: 0.82 / Rpim(I) all: 0.632 / Rrim(I) all: 1.363 / % possible all: 57.9

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
autoPROC1.1.7data processing
Aimless0.7.7data scaling
STARANISO2.3.74data scaling
XDSBUILT=20220820data reduction
PHASERphasing
Coot0.9.8.95model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→63.63 Å / SU ML: 0.3004 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.0938
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.253 1118 5.12 %
Rwork0.1951 20711 -
obs0.1976 21829 74.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.48 Å2
Refinement stepCycle: LAST / Resolution: 2.72→63.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6404 0 66 32 6502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00296598
X-RAY DIFFRACTIONf_angle_d0.52898919
X-RAY DIFFRACTIONf_chiral_restr0.03721017
X-RAY DIFFRACTIONf_plane_restr0.00391102
X-RAY DIFFRACTIONf_dihedral_angle_d19.27462489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.840.4058220.268252X-RAY DIFFRACTION7.57
2.84-2.990.3062590.31131075X-RAY DIFFRACTION31.35
2.99-3.180.31781100.28712104X-RAY DIFFRACTION61.81
3.18-3.420.32761970.26533339X-RAY DIFFRACTION97.68
3.42-3.770.28781850.20873444X-RAY DIFFRACTION99.92
3.77-4.310.25531600.17933489X-RAY DIFFRACTION99.92
4.31-5.430.24341890.15353463X-RAY DIFFRACTION99.89
5.43-63.630.20511960.18013545X-RAY DIFFRACTION99.6
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)
11.757710232350.906174886724-0.8286577501521.28787107328-0.6250798577461.786924000570.231232632453-0.06130311086080.297935108620.345036000671-0.2773687981170.213730412104-0.4412409020060.114402237871-0.3266847318310.288833309922-0.1138499197130.05154179926730.3099839480220.07438846907610.369808709731-32.0256955866-30.648431658914.9509085428
22.5318094789-0.8496388738940.3967166423091.81530771444-0.6355850510824.413906860240.110727869001-0.164654098216-0.2729182667060.0244253230593-0.169395812855-0.3820914751160.3845259393360.156220701835-0.04496781188860.2886415222980.03921043234980.07160361800320.1906348638870.05853177566490.415750668449-23.7160632967-39.8689532884.27518469777
33.329877921350.830090803559-0.1622314030821.45420320017-0.9285790217836.347424991040.07580385764450.08767809036670.111778275421-0.274454574025-0.0833537527625-0.2195929942050.2618917508481.204856874660.189634786130.331559460692-0.006950487923940.07229118280360.6355086476430.2315188336250.560805129156-14.8123621466-32.1283509116-4.02659305302
42.714906589390.584697440537-0.2736966466692.099766521450.02277343170992.18151708079-0.01252726731830.184901523197-0.168806336865-0.116743817495-0.166280812688-0.754922509492-0.02108440927340.9626454042830.009604447269760.4231658330190.1905895440410.10867830610.6998199779920.2523467473260.475481069684-7.61948560774-16.8282925499-26.911167084
51.962983397430.02440912575720.3632435251642.32387313581-0.397363736591.910728676520.03388343092980.192267418991-0.108665042901-0.233376657581-0.08552860311570.1440153852210.2154128190390.009212842687940.009496750279180.4092483121690.1660572673110.1043345282570.3100319377330.0405217995670.310356877544-26.2492924397-24.1862870109-21.4538404649
60.605145389990.3927151271970.1769271556931.09278203433-0.001638283805260.4603878776490.254656398575-0.493504229571-0.1178008678160.42776690835-0.329020421116-0.168552228734-0.08319521856150.411568792990.04285795051380.588875499825-0.428632708022-0.1261496233560.7676661509410.3430001003010.345352464827-17.7231242439-38.284370206431.0428109461
71.6614679111-1.427193444660.5309227532652.10014936266-0.2638978677430.8577567938420.157334501067-0.600753740954-0.166317833866-0.0790764300647-0.271602196099-0.6691751521620.605457856920.8977499267720.1685415652520.709322191687-0.02468765725390.02623922800780.9802711658560.2607178847940.775129182559-10.0042968631-38.145365883823.3132041648
82.79845823954-0.811909195397-0.1453292296060.4689062410960.631753705881.471250295950.413322611625-0.00188319331918-0.340921738740.6235258925820.05747451305540.2924382328290.0008374068478860.3051765391-0.1691730387730.670527891979-0.175912029616-0.009467978017750.5237232215520.2364670081430.589058140112-27.0969292239-44.526242710129.3888615468
95.016926969630.0221583206841-0.3496934453673.49937604603-1.021387610060.8103143831620.360567915775-0.4927363157220.7238409644841.05903250045-0.554546023837-0.417908782715-0.5128773749980.5615502397760.1541528703051.12873947711-0.470677327947-0.07630419343010.6981114821640.1722726332870.701440725215-17.2233496708-23.687245722934.703794687
103.759751596740.891971785015-0.2263380729793.42731513253-0.1947971231011.122369458870.0108555600336-0.5516345269340.1077643456330.985296795757-0.43131239097-0.200323232741-0.2111739302880.4383305823020.2571437195840.724983122362-0.381575083303-0.06322230777120.6927906046690.2014650621090.541179789674-21.8048419894-33.03563682737.3176270521
117.607144505360.4692504170172.454681932171.27161735068-0.4668170636811.10267480443-0.274798230218-0.5298550839840.8642020645360.344717258623-0.240584274743-0.452205845423-1.024594899320.6335825375290.8889259513571.1031644593-0.423777259-0.3905141179861.013440403640.05807522471040.629153977616-18.6491968465-29.694179640644.8119048507
126.38037678959-0.1869401370120.4145812615763.94431062113-0.6924031265921.478270075930.043247424416-1.260670999970.01483832560460.43431500863-0.1814547581690.418058782764-0.8032945323070.6121878314670.3119139831090.623975789787-0.127841417667-0.1271806095380.8522354782020.2579550401120.637750319184-24.6736571443-37.093666358241.4638722245
130.6300124699321.14433460278-0.815731709632.61331429398-0.5376572146462.75567775444-0.458554220993-0.684150992696-0.08456422715240.711031177396-0.133331436999-1.16461472396-0.1818133967741.099796838670.05994773820030.923640242784-0.189206373876-0.4017161899621.206522387520.3855479391660.967567987146-2.50006416844-40.218198147142.038388981
140.033488206105-0.1453798644280.1487933178072.11876827317-0.8430399625210.6670217963190.144046956313-0.509039338919-0.1397007655531.1231883435-0.508975616571-0.847891544767-0.4573860299280.674965126840.06296419335640.861889828852-0.281116262868-0.1950991865591.147739328980.4863362377750.680689683059-15.0377167841-42.518981782246.5436417272
150.2815105961590.0569693193731-0.05359188305211.92746317359-0.7161797868122.77325691545-0.0499817889771-0.202113458813-0.2018161153310.606910938221-0.230895647704-0.1050111298230.3834104973420.3466556001150.7568232356830.732502100567-0.1618708393820.1170624136510.5949691086760.5599796959390.589332747632-21.4105816228-48.744054014836.5396935803
160.06615140521540.0262160785352-0.03835050739260.0747214555518-0.01426755799760.0203733668548-0.07036319563160.00385940114633-0.008443728636110.04540040117630.03673899470770.113164983379-0.0881699636583-0.0330684202704-0.5246358455020.4519862795390.1446814121980.2885994447870.2432060418160.3736834575570.0670256359862-22.0477509445-1.3876506061-38.3312327438
171.957054301991.39559402844-0.1894848414962.86310768041-1.20683016471.599548599650.04482199459770.337546458566-0.5690736687810.4208334912990.06186629048241.02976339301-0.422656560108-0.552179422317-0.1881676570790.4661223758670.137027772630.04882740432860.7824670184520.2646711771971.01564151633-29.3040527242-1.91051813736-31.1793015825
182.56585238486-0.48250964854-0.1236005484494.23900057146-1.355422252171.677907701810.194590100340.2967772110390.0722805506884-0.276459677619-0.333488104879-0.307232650955-0.01928116035120.637986391410.1842906847440.4502554172710.1533665477880.1519821329150.5211084923810.2139301519940.334151793609-15.0318806892-1.32747554304-38.0028908372
197.79444420322-1.44250084128-2.512484643851.344255614612.036484335773.108910400450.344753887320.1851325824520.709173942443-0.128703475014-0.569837385552-1.25778625091-0.8858871843410.8594740833990.08494665429420.57893680873-0.15802278169-0.0868118661770.785097217840.400846027110.837200736552-11.740917553711.2360902722-41.1128093713
202.295322942541.683553421-0.8551884551731.380865455270.03660118380393.451212400340.01259660902260.4707018754570.8587367338650.185060281096-0.387116148259-0.251552094209-0.566196347248-0.371875191695-0.06333923283740.7687108457430.0452288870186-0.0003439196029650.6896659581030.3443763887390.613761918904-24.3504791079.42463017111-44.1259362795
210.6173402297490.296909713781-0.3141137264170.5288184154340.4115048263740.99016525657-0.01256777446440.2293264262320.151086415159-0.611153019573-0.087470297846-0.153708268101-0.4643414657750.4485565747540.8744310195621.121581367280.2613897088680.03324343154141.223097460270.6605147908340.423814243994-17.496303452910.53392798-52.0432106281
221.47222792250.290579085954-1.747563594165.15870103180.6686545577952.2813662529-0.0701242878060.6815003030380.15217523842-1.218613426510.03119816245580.4294389835450.681980126710.125245331097-0.2225579033910.5881359147260.125410041186-0.04349292332691.057277246730.3293872712740.414016953748-24.2626950684-2.89390859634-49.3521884795
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 154 )AA7 - 1541 - 148
22chain 'A' and (resid 155 through 233 )AA155 - 233149 - 214
33chain 'A' and (resid 234 through 254 )AA234 - 254215 - 235
44chain 'B' and (resid 7 through 122 )BB7 - 1221 - 112
55chain 'B' and (resid 123 through 254 )BB123 - 254113 - 236
66chain 'C' and (resid 5 through 25 )CC5 - 251 - 21
77chain 'C' and (resid 26 through 39 )CC26 - 3922 - 35
88chain 'C' and (resid 40 through 62 )CC40 - 6236 - 58
99chain 'C' and (resid 63 through 72 )CC63 - 7259 - 68
1010chain 'C' and (resid 73 through 90 )CC73 - 9069 - 86
1111chain 'C' and (resid 91 through 106 )CC91 - 10687 - 102
1212chain 'C' and (resid 107 through 120 )CC107 - 120103 - 113
1313chain 'C' and (resid 121 through 131 )CC121 - 131114 - 124
1414chain 'C' and (resid 132 through 153 )CC132 - 153125 - 146
1515chain 'C' and (resid 154 through 168 )CC154 - 168147 - 161
1616chain 'F' and (resid 6 through 25 )FF6 - 251 - 20
1717chain 'F' and (resid 26 through 39 )FF26 - 3921 - 34
1818chain 'F' and (resid 40 through 90 )FF40 - 9035 - 79
1919chain 'F' and (resid 91 through 106 )FF91 - 10680 - 95
2020chain 'F' and (resid 107 through 131 )FF107 - 13196 - 115
2121chain 'F' and (resid 132 through 148 )FF132 - 148116 - 132
2222chain 'F' and (resid 149 through 168 )FF149 - 168133 - 152

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