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- PDB-3nmx: Crystal structure of APC complexed with Asef -

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Basic information

Entry
Database: PDB / ID: 3nmx
TitleCrystal structure of APC complexed with Asef
Components
  • APC variant protein
  • Rho guanine nucleotide exchange factor 4
KeywordsCELL ADHESION/CELL CYCLE / protein-protein complex / CELL ADHESION-CELL CYCLE complex
Function / homology
Function and homology information


cellular component organization / APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / intracellular organelle / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome / pattern specification process ...cellular component organization / APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / intracellular organelle / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome / pattern specification process / bicellular tight junction assembly / protein kinase regulator activity / negative regulation of microtubule depolymerization / negative regulation of cyclin-dependent protein serine/threonine kinase activity / filopodium assembly / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / microtubule plus-end binding / beta-catenin destruction complex / regulation of microtubule-based process / heart valve development / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / catenin complex / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / cell fate specification / regulation of small GTPase mediated signal transduction / lamellipodium assembly / endocardial cushion morphogenesis / dynein complex binding / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of Wnt signaling pathway / NRAGE signals death through JNK / mitotic spindle assembly checkpoint signaling / Apoptotic cleavage of cellular proteins / regulation of cell differentiation / CDC42 GTPase cycle / mitotic cytokinesis / RHOA GTPase cycle / bicellular tight junction / lateral plasma membrane / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / cell periphery / Deactivation of the beta-catenin transactivating complex / adherens junction / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / kinetochore / ruffle membrane / beta-catenin binding / Wnt signaling pathway / positive regulation of protein catabolic process / G alpha (12/13) signalling events / cell migration / Ovarian tumor domain proteases / lamellipodium / insulin receptor signaling pathway / nervous system development / positive regulation of cold-induced thermogenesis / microtubule binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex assembly / microtubule / cell adhesion / positive regulation of cell migration / intracellular signal transduction / positive regulation of apoptotic process / protein domain specific binding / negative regulation of cell population proliferation / centrosome / DNA damage response / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP / Unstructured region on APC between SAMP and APC_crr / Unstructured region on APC between APC_crr regions 5 and 6 / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding ...Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP / Unstructured region on APC between SAMP and APC_crr / Unstructured region on APC between APC_crr regions 5 and 6 / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain / Adenomatous polyposis coli protein, 15 residue repeat / Adenomatous polyposis coli (APC) family / Adenomatous polyposis coli protein / Adenomatous polyposis coli, N-terminal dimerisation domain / APC, N-terminal coiled-coil domain superfamily / Adenomatous polyposis coli (APC) repeat / APC repeat / SAMP Motif / EB-1 Binding Domain / APC basic domain / APC 15 residue motif / Coiled-coil N-terminus of APC, dimerisation domain / Adenomatous polyposis coli (APC) repeat / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / 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. / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Armadillo-like helical / Alpha Horseshoe / PH-like domain superfamily / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Adenomatous polyposis coli protein / APC variant protein / Rho guanine nucleotide exchange factor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsZhang, Z. / Chen, L. / Gao, L. / Lin, K. / Wu, G.
CitationJournal: Cell Res. / Year: 2012
Title: Structural basis for the recognition of Asef by adenomatous polyposis coli.
Authors: Zhang, Z. / Chen, L. / Gao, L. / Lin, K. / Zhu, L. / Lu, Y. / Shi, X. / Gao, Y. / Zhou, J. / Xu, P. / Zhang, J. / Wu, G.
History
DepositionJun 22, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 15, 2017Group: Database references
Revision 1.3Dec 25, 2019Group: Advisory / Database references / Derived calculations
Category: citation / pdbx_struct_special_symmetry ...citation / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: APC variant protein
B: APC variant protein
C: APC variant protein
D: Rho guanine nucleotide exchange factor 4
E: Rho guanine nucleotide exchange factor 4
F: Rho guanine nucleotide exchange factor 4


Theoretical massNumber of molelcules
Total (without water)125,4636
Polymers125,4636
Non-polymers00
Water9,314517
1
A: APC variant protein
D: Rho guanine nucleotide exchange factor 4


Theoretical massNumber of molelcules
Total (without water)41,8212
Polymers41,8212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-5 kcal/mol
Surface area15880 Å2
MethodPISA
2
B: APC variant protein
E: Rho guanine nucleotide exchange factor 4


Theoretical massNumber of molelcules
Total (without water)41,8212
Polymers41,8212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-6 kcal/mol
Surface area15860 Å2
MethodPISA
3
C: APC variant protein
F: Rho guanine nucleotide exchange factor 4


Theoretical massNumber of molelcules
Total (without water)41,8212
Polymers41,8212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-7 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.790, 92.180, 107.840
Angle α, β, γ (deg.)90.000, 93.770, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-173-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13D
23E
14F
24D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A407 - 730
2114B407 - 730
1124A407 - 731
2124C407 - 731
1134D180 - 195
2134E180 - 195
1144F180 - 195
2144D180 - 195

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein APC variant protein / Adenomatous Polyposis Coli


Mass: 39268.246 Da / Num. of mol.: 3 / Fragment: Armadiilo repeats domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4LE70, UniProt: P25054*PLUS
#2: Protein/peptide Rho guanine nucleotide exchange factor 4 / APC-stimulated guanine nucleotide exchange factor / Asef


Mass: 2552.648 Da / Num. of mol.: 3 / Fragment: UNP residues 170-194 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NR80
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 2.92 Å3/Da / Density % sol: 57.89 % / Mosaicity: 0.401 °
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 25% PEG 1500, 0.1M NaCl, pH 9.0, vapor diffusion, hanging drop, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97939 Å
DetectorDetector: CCD / Date: Apr 4, 2010
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 60878 / % possible obs: 95.1 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.068 / Χ2: 1.004 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.384.90.27645590.998172.2
2.38-2.485.30.26954000.994184.4
2.48-2.596.30.26760411.008195.1
2.59-2.737.30.2463671.007199.6
2.73-2.97.70.17663960.9931100
2.9-3.127.70.1263671.0041100
3.12-3.447.70.07963941.0061100
3.44-3.937.80.06764191.0061100
3.93-4.957.70.0664161.0081100
4.95-507.60.03865191.006199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.898 / Occupancy max: 1 / Occupancy min: 0 / SU B: 16.491 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25435 2923 5 %RANDOM
Rwork0.20753 ---
obs0.20987 54971 90.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 53.81 Å2 / Biso mean: 36.238 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.04 Å2
2--0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7801 0 0 517 8318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0217906
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8231.95310676
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.77351004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.92824.746335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.294151457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9961545
X-RAY DIFFRACTIONr_chiral_restr0.0570.21252
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025748
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1631.55017
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.31928002
X-RAY DIFFRACTIONr_scbond_it0.47632889
X-RAY DIFFRACTIONr_scangle_it0.7514.52674
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2420medium positional0.340.5
2A2413medium positional0.360.5
3D90medium positional0.260.5
4F90medium positional0.180.5
1B2420medium thermal0.182
2C2413medium thermal0.162
3E90medium thermal0.232
4D90medium thermal0.132
LS refinement shellResolution: 2.304→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 61 -
Rwork0.215 900 -
all-963 -
obs--20.46 %
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)
15.2018-0.624-0.63881.07630.24311.76840.02680.22260.1896-0.0151-0.0135-0.12520.06040.1147-0.01320.18730.0025-0.00170.09030.01360.031413.00282.5488-15.7978
21.4556-1.2005-0.26555.5241-0.23231.44490.09150.088-0.1238-0.43860.04520.42520.0306-0.3243-0.13680.0544-0.0454-0.03280.15250.02840.059629.0432-15.2529-51.2705
33.4954-2.75771.94215.0368-2.31782.5043-0.1808-0.4818-0.53890.65640.63280.7067-0.1948-0.6002-0.4520.2605-0.02310.08030.28940.14450.174337.091-41.5705-20.7352
411.0547-6.1495-4.95063.65891.65939.9819-0.0042-1.30280.65860.01590.6957-0.4721-0.93340.6386-0.69160.2622-0.07580.18760.2416-0.08490.36676.63633.4002-5.1392
54.15210.70662.30919.2588-1.29694.93360.0490.0420.23120.60460.24040.8609-0.1205-0.7086-0.28940.05680.03170.03820.17040.04840.155729.7567-22.688-41.4703
620.5882-4.37257.81326.1057-4.592913.7930.7880.428-1.55280.00470.33110.41190.9462-0.733-1.11920.2393-0.02270.02260.12920.02470.248433.9538-35.6634-31.2718
70.447-0.1813-0.18640.29690.15220.12890.029-0.0225-0.01340.00290.01650.0196-0.0172-0.0587-0.04560.2907-0.0185-0.03950.30380.04410.307125.8224-14.9923-31.924
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A403 - 736
2X-RAY DIFFRACTION2B403 - 737
3X-RAY DIFFRACTION3C403 - 737
4X-RAY DIFFRACTION4D180 - 192
5X-RAY DIFFRACTION5E180 - 192
6X-RAY DIFFRACTION6F180 - 192
7X-RAY DIFFRACTION7A4 - 395

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