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

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Basic information

Entry
Database: PDB / ID: 3nmz
TitleCrystal structure of APC complexed with Asef
Components
  • APC variant protein
  • Rho guanine nucleotide exchange factor 4
KeywordsCELL ADHESION/CELL CYCLE / protein-protein complex / armadillo repeats / 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 / SH3 Domains / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Armadillo-like helical / Alpha Horseshoe / PH-like domain superfamily / Armadillo-type fold / Roll / Mainly Beta / 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: 3.01 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 23, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2016Group: Structure summary
Revision 1.3Mar 15, 2017Group: Database references
Revision 1.4Dec 25, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.5Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
D: Rho guanine nucleotide exchange factor 4
C: Rho guanine nucleotide exchange factor 4


Theoretical massNumber of molelcules
Total (without water)126,8184
Polymers126,8184
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-35 kcal/mol
Surface area43800 Å2
MethodPISA
2
A: APC variant protein
C: Rho guanine nucleotide exchange factor 4


Theoretical massNumber of molelcules
Total (without water)63,4092
Polymers63,4092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-11 kcal/mol
Surface area23540 Å2
MethodPISA
3
B: APC variant protein
D: Rho guanine nucleotide exchange factor 4


Theoretical massNumber of molelcules
Total (without water)63,4092
Polymers63,4092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-13 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.175, 163.175, 242.593
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12D
22C

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSARGARGAA327 - 73346 - 452
21LYSLYSARGARGBB327 - 73346 - 452
12TYRTYRGLNGLNDC175 - 25415 - 94
22TYRTYRGLNGLNCD175 - 25415 - 94

NCS ensembles :
ID
1
2

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Components

#1: Protein APC variant protein / Adenomatous Polyposis Coli


Mass: 50767.340 Da / Num. of mol.: 2 / Fragment: Armadiilo repeats domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APC variant protein / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4LE70, UniProt: P25054*PLUS
#2: Protein Rho guanine nucleotide exchange factor 4 / APC-stimulated guanine nucleotide exchange factor / Asef


Mass: 12641.560 Da / Num. of mol.: 2 / Fragment: UNP residues 170-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF4, KIAA1112 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NR80
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 4.9 Å3/Da / Density % sol: 74.9 % / Mosaicity: 0.208 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1M lithium sulfate, 0.5M ammonium sulfate, pH 5.6, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorDetector: CCD / Date: Mar 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 46293 / % possible obs: 96.1 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.057 / Χ2: 0.996 / Net I/σ(I): 15.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3-3.114.30.40633470.938169.2
3.11-3.234.60.39544360.96192.3
3.23-3.385.60.29947920.999199.9
3.38-3.565.90.19248250.9931100
3.56-3.785.90.11148140.9911100
3.78-4.075.90.07348141.0031100
4.07-4.485.90.05448161.0091100
4.48-5.135.90.04648511.0211100
5.13-6.465.90.04548011.0021100
6.46-505.80.04147971.001199.5

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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
Starting model: 3NMW, 2PZ1

3nmw

2pz1


Resolution: 3.01→50 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.86 / Occupancy max: 1 / Occupancy min: 0.11 / SU B: 48.386 / SU ML: 0.386 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2839 2202 5.1 %RANDOM
Rwork0.2487 ---
obs0.2505 43230 90.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.32 Å2 / Biso mean: 82.824 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 3.01→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7546 0 0 127 7673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0217663
X-RAY DIFFRACTIONr_angle_refined_deg0.8611.94510345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.15967
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.63424.432352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.616151385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0881556
X-RAY DIFFRACTIONr_chiral_restr0.0570.21171
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025700
X-RAY DIFFRACTIONr_mcbond_it0.0721.54826
X-RAY DIFFRACTIONr_mcangle_it0.14427697
X-RAY DIFFRACTIONr_scbond_it0.2432837
X-RAY DIFFRACTIONr_scangle_it0.4164.52648
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3072MEDIUM POSITIONAL0.440.5
1A3072MEDIUM THERMAL0.12
2D627MEDIUM POSITIONAL0.360.5
2D627MEDIUM THERMAL0.082
LS refinement shellResolution: 3.007→3.085 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 21 -
Rwork0.319 501 -
all-522 -
obs--14.7 %
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)
13.43251.4287-2.58692.6017-2.31314.7329-0.5373-0.06070.23150.2390.0221-0.1345-0.13320.17520.51520.36210.0354-0.20220.4114-0.24810.392943.4316-34.2145-14.8252
23.3822-1.1091.58292.9552-2.09964.6752-0.4040.5343-0.15820.0488-0.06510.015-0.26920.33410.46910.1176-0.11670.02970.6104-0.39150.397342.6006-51.4974-44.0494
310.4319-1.8688-2.60472.28961.81848.2571-0.17650.6026-0.5826-0.2106-0.05770.7959-0.1369-0.58910.23420.0848-0.0532-0.11990.7791-0.38220.605520.598-48.2576-39.1566
49.1334-0.32161.37144.72631.17176.0196-0.3231-0.01820.7840.46980.01410.7371-0.4973-0.45350.3090.31240.1716-0.05930.6774-0.27950.496621.7371-32.7538-21.6634
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A326 - 736
2X-RAY DIFFRACTION2B326 - 733
3X-RAY DIFFRACTION3D172 - 255
4X-RAY DIFFRACTION4C171 - 255

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