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- PDB-3lge: Crystal structure of rabbit muscle aldolase-SNX9 LC4 complex -

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Basic information

Entry
Database: PDB / ID: 3lge
TitleCrystal structure of rabbit muscle aldolase-SNX9 LC4 complex
Components
  • Fructose-bisphosphate aldolase A
  • Sorting nexin-9
KeywordsLyase/protein binding / complex / glycolysis / actin dynamics / LC4 / hydrophobic pocket / Acetylation / Lyase / Phosphoprotein / Schiff base / Protein transport / SH3 domain / Transport / Lyase-protein binding complex
Function / homology
Function and homology information


lipid tube assembly / cuticular plate / plasma membrane tubulation / 1-phosphatidylinositol binding / Arp2/3 complex binding / negative regulation of Arp2/3 complex-mediated actin nucleation / cleavage furrow formation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / positive regulation of membrane protein ectodomain proteolysis ...lipid tube assembly / cuticular plate / plasma membrane tubulation / 1-phosphatidylinositol binding / Arp2/3 complex binding / negative regulation of Arp2/3 complex-mediated actin nucleation / cleavage furrow formation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / positive regulation of membrane protein ectodomain proteolysis / M band / I band / clathrin-coated vesicle / regulation of synaptic vesicle endocytosis / endosomal transport / Golgi Associated Vesicle Biogenesis / positive regulation of actin filament polymerization / mitotic cytokinesis / positive regulation of protein kinase activity / clathrin-coated pit / ruffle / receptor-mediated endocytosis / phosphatidylinositol binding / glycolytic process / intracellular protein transport / trans-Golgi network / cytoplasmic vesicle membrane / positive regulation of GTPase activity / endocytosis / presynapse / Clathrin-mediated endocytosis / cytoplasmic vesicle / protein homotetramerization / protein-containing complex assembly / positive regulation of cell migration / cadherin binding / ubiquitin protein ligase binding / protein homodimerization activity / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SNX9, SH3 domain / Sorting nexin-9, BAR domain / Sorting nexin-9, PX domain / Sorting nexin 9 family / Sorting nexin protein, WASP-binding domain / WASP-binding domain of Sorting nexin protein / Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I ...SNX9, SH3 domain / Sorting nexin-9, BAR domain / Sorting nexin-9, PX domain / Sorting nexin 9 family / Sorting nexin protein, WASP-binding domain / WASP-binding domain of Sorting nexin protein / Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Fructose-bisphosphate aldolase A / Sorting nexin-9
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsRangarajan, E.S. / Park, H. / Fortin, E. / Sygusch, J. / Izard, T.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Mechanism of aldolase control of sorting nexin 9 function in endocytosis.
Authors: Rangarajan, E.S. / Park, H. / Fortin, E. / Sygusch, J. / Izard, T.
History
DepositionJan 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 6, 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
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: Fructose-bisphosphate aldolase A
B: Fructose-bisphosphate aldolase A
C: Fructose-bisphosphate aldolase A
D: Fructose-bisphosphate aldolase A
E: Sorting nexin-9
F: Sorting nexin-9
G: Sorting nexin-9
H: Sorting nexin-9


Theoretical massNumber of molelcules
Total (without water)171,1138
Polymers171,1138
Non-polymers00
Water30,8781714
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.028, 118.175, 175.896
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
Fructose-bisphosphate aldolase A / Muscle-type aldolase


Mass: 39263.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ALDOA / Plasmid: PPB1 / Production host: Escherichia coli (E. coli) / Strain (production host): Dh5alphamcr / References: UniProt: P00883, fructose-bisphosphate aldolase
#2: Protein/peptide
Sorting nexin-9 / / SH3 and PX domain-containing protein 1 / Protein SDP1 / SH3 and PX domain-containing protein 3A


Mass: 3514.459 Da / Num. of mol.: 4 / Fragment: UNP residues 152-182 / Source method: obtained synthetically / Details: This sequence occurs naturally in Humans / References: UniProt: Q9Y5X1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1714 / 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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG-MME 550, MgCl2, pH 7, Vapor Diffusion, Hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 5.9 % / Av σ(I) over netI: 10.37 / Number: 542298 / Rmerge(I) obs: 0.143 / Χ2: 0.96 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 91354 / % possible obs: 98.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.745099.810.0630.9766.6
3.764.7410010.0881.1976.8
3.293.7610010.1060.9556.9
2.993.2910010.1430.7836.9
2.772.9910010.1940.7816.9
2.612.7710010.2650.9516.7
2.482.6199.910.3070.8446.2
2.372.4899.410.3730.915.1
2.282.3797.710.4390.8813.9
2.22.2889.810.5261.9072.9
ReflectionResolution: 2.2→50 Å / Num. all: 92559 / Num. obs: 91509 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.143 / Χ2: 0.958 / Net I/σ(I): 4.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.282.90.52682161.90789.8
2.28-2.373.90.43989220.88197.7
2.37-2.485.10.37391130.9199.4
2.48-2.616.20.30791550.84499.9
2.61-2.776.70.26591730.951100
2.77-2.996.90.19492110.781100
2.99-3.296.90.14392320.783100
3.29-3.766.90.10693070.955100
3.76-4.746.80.08893411.197100
4.74-506.60.06396840.97699.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.11.0refinement
SCALEPACKdata scaling
MOLREPphasing
TNTrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OT0

2ot0


Resolution: 2.2→48.88 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.189 4580 5.01 %RANDOM
Rwork0.151 ---
all0.153 91509 --
obs0.153 91491 98.76 %-
Displacement parametersBiso max: 124.31 Å2 / Biso mean: 24.643 Å2 / Biso min: 6.86 Å2
Baniso -1Baniso -2Baniso -3
1-7.583 Å20 Å20 Å2
2---3.247 Å20 Å2
3----4.337 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11178 0 0 1714 12892
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg0.97
X-RAY DIFFRACTIONo_bond_d0.01
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 297 4.94 %
Rwork0.227 5720 -
all0.229 6017 -
obs-6017 98.76 %
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)
10.6408-0.03970.08150.88130.18330.48190.0016-0.1088-0.03710.1870.0221-0.11620.08780.031-0.02370.09720.014-0.025-0.1310.0056-0.1188-25.9369-16.510662.1018
20.5257-0.1379-0.12930.60870.12950.28670.0153-0.05080.02350.0337-0.01460.0568-0.0163-0.0086-0.00080.0773-0.00850.0052-0.1088-0.0263-0.0739-64.9901-1.121460.3326
30.39210.17090.09170.65180.13360.21630.0045-0.00150.0262-0.0097-0.01150.07270.0068-0.02890.00690.0867-0.00270.0097-0.1037-0.0091-0.0745-67.8299-31.8732.4799
40.45550.0392-0.10310.4207-0.01020.4954-0.01190.03490.0411-0.08010.014-0.029-0.02590.0178-0.00210.1017-0.00640.0049-0.12740.0089-0.0794-29.8072-16.521422.603
50.36970.581-2.5151.8729-0.64222.5969-0.0018-0.02160.0953-0.04710.08160.0094-0.01330.0729-0.07980.0997-0.00630.0077-0.1123-0.0619-0.0391-64.852214.571656.0271
61.87510.16731.90531.28420.73631.1229-0.0113-0.0401-0.1220.04230.06270.0194-0.01540.0244-0.05130.07710.0147-0.0059-0.0726-0.0097-0.0482-66.916-47.625536.6551
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 1743
2X-RAY DIFFRACTION2B1 - 1831
3X-RAY DIFFRACTION3C1 - 2039
4X-RAY DIFFRACTION4D1 - 2064
5X-RAY DIFFRACTION5F164 - 182
6X-RAY DIFFRACTION6G164 - 182

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