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- PDB-9uvl: Crystal structure of AGAP1-GDP complex -

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Basic information

Entry
Database: PDB / ID: 9uvl
TitleCrystal structure of AGAP1-GDP complex
ComponentsArf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
KeywordsCELL INVASION / Triple-negative breast cancer / AGAP1 / noncanonical GDP binding / carcinogenesis / structure biology
Function / homology
Function and homology information


postsynaptic endosome / regulation of modification of postsynaptic structure / GTPase activator activity / phospholipid binding / protein transport / GTPase activity / GTP binding / zinc ion binding
Similarity search - Function
: / GTP-binding protein-like domain (GLD) profile. / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / PH domain profile. / Pleckstrin homology domain. ...: / GTP-binding protein-like domain (GLD) profile. / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Rab subfamily of small GTPases / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsZhang, S. / Zhang, Y. / Cheng, N. / Wang, J. / Li, Z. / Meng, G. / Zhang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81970132 China
CitationJournal: Cell.Mol.Life Sci. / Year: 2026
Title: AGAP1 and noncanonical GDP binding regulate triple-negative breast cancer development.
Authors: Zhang, Y. / Zhang, S. / Deng, X. / Cheng, N. / Wang, J. / Huang, H. / Zhuo, Z. / Ye, S. / Yu, X. / Li, Z. / Meng, G. / Zhang, H.
History
DepositionMay 10, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2026Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Apr 29, 2026Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 17, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
B: Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
C: Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
D: Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
E: Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
F: Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
G: Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
H: Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,89537
Polymers154,8398
Non-polymers4,05629
Water1,15364
1
A: Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)19,3551
Polymers19,3551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3638
Polymers19,3551
Non-polymers1,0087
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)19,3551
Polymers19,3551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3638
Polymers19,3551
Non-polymers1,0087
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3879
Polymers19,3551
Non-polymers1,0328
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8474
Polymers19,3551
Non-polymers4923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8715
Polymers19,3551
Non-polymers5164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)19,3551
Polymers19,3551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.405, 124.678, 127.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1 / AGAP-1 / Centaurin-gamma-2 / Cnt-g2 / GTP-binding and GTPase-activating protein 1 / GGAP1


Mass: 19354.912 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGAP1, CENTG2, KIAA1099 / Production host: Escherichia phage EcSzw_1 (virus) / References: UniProt: Q9UPQ3
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 298 K / Method: liquid diffusion
Details: 10% w/v PEG 4000, 20% w/v 2-Propanol, 100 mM HEPES Sodium Salt, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Mar 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.49→35.17 Å / Num. obs: 62085 / % possible obs: 96.2 % / Redundancy: 5.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.3
Reflection shellResolution: 2.49→2.579 Å / Rmerge(I) obs: 1.57 / Num. unique obs: 5649 / CC1/2: 0.685

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→35.17 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 30.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 3144 5.06 %
Rwork0.219 --
obs0.221 62085 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.49→35.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10407 0 245 64 10716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01810852
X-RAY DIFFRACTIONf_angle_d2.2814763
X-RAY DIFFRACTIONf_dihedral_angle_d15.436460
X-RAY DIFFRACTIONf_chiral_restr0.1761643
X-RAY DIFFRACTIONf_plane_restr0.0131876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.5250.3535840.36232042X-RAY DIFFRACTION73
2.525-2.56640.34511320.3412620X-RAY DIFFRACTION95
2.5664-2.61060.30761220.31092653X-RAY DIFFRACTION95
2.6106-2.65810.29391430.29912656X-RAY DIFFRACTION96
2.6581-2.70920.36851480.30132622X-RAY DIFFRACTION96
2.7092-2.76450.38261630.29112627X-RAY DIFFRACTION96
2.7645-2.82460.36731490.29132655X-RAY DIFFRACTION96
2.8246-2.89020.33391480.29392621X-RAY DIFFRACTION95
2.8902-2.96250.3391480.30592641X-RAY DIFFRACTION96
2.9625-3.04250.36991390.29122658X-RAY DIFFRACTION96
3.0425-3.1320.35391470.2642664X-RAY DIFFRACTION96
3.132-3.2330.36161580.25882671X-RAY DIFFRACTION97
3.233-3.34850.31651220.24112712X-RAY DIFFRACTION97
3.3485-3.48250.2481270.24192729X-RAY DIFFRACTION98
3.4825-3.64080.31261320.23012584X-RAY DIFFRACTION92
3.6408-3.83250.27151850.23172728X-RAY DIFFRACTION99
3.8325-4.07230.26481330.2052821X-RAY DIFFRACTION100
4.0723-4.38620.23961480.17972798X-RAY DIFFRACTION100
4.3862-4.82660.19641380.16122847X-RAY DIFFRACTION100
4.8266-5.52270.22561640.1772817X-RAY DIFFRACTION100
5.5227-6.94920.24161640.22352827X-RAY DIFFRACTION99
6.9492-35.1670.23811500.18862948X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 34.4074 Å / Origin y: 37.505 Å / Origin z: 105.349 Å
111213212223313233
T0.5494 Å20.0087 Å20.0054 Å2-0.5798 Å2-0.0055 Å2--0.6004 Å2
L-0.0106 °20.048 °20.0043 °2-0.0461 °20.097 °2--0.0983 °2
S-0.0032 Å °-0.0321 Å °-0.0158 Å °-0.0052 Å °-0.0244 Å °0.0235 Å °-0.0163 Å °0.0585 Å °-0 Å °
Refinement TLS groupSelection details: ALL

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