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- PDB-3v2o: Crystal Structure of the Peptide Bound Complex of the Ankyrin Rep... -

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Basic information

Entry
Database: PDB / ID: 3v2o
TitleCrystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2
Components
  • Ankyrin repeat family A protein 2
  • Low-density lipoprotein receptor-related protein 2
KeywordsPROTEIN BINDING / Structural Genomics Consortium / SGC / ANKRA2 / ANK repeat / LRP2/megalin
Function / homology
Function and homology information


endocytic hemoglobin import into cell / chemoattraction of axon / Transport of RCbl within the body / Retinoid metabolism and transport / diol metabolic process / positive regulation of oligodendrocyte progenitor proliferation / pulmonary artery morphogenesis / secondary heart field specification / positive regulation of lysosomal protein catabolic process / folate import across plasma membrane ...endocytic hemoglobin import into cell / chemoattraction of axon / Transport of RCbl within the body / Retinoid metabolism and transport / diol metabolic process / positive regulation of oligodendrocyte progenitor proliferation / pulmonary artery morphogenesis / secondary heart field specification / positive regulation of lysosomal protein catabolic process / folate import across plasma membrane / Vitamin D (calciferol) metabolism / metanephric proximal tubule development / negative regulation of endopeptidase activity / protein transporter activity / positive regulation of lipoprotein transport / ventricular compact myocardium morphogenesis / response to leptin / transcytosis / metal ion transport / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / vitamin D metabolic process / cranial skeletal system development / neuron projection arborization / coronary artery morphogenesis / insulin-like growth factor I binding / protein import / coronary vasculature development / outflow tract septum morphogenesis / positive regulation of neurogenesis / response to vitamin D / cargo receptor activity / endosomal transport / aorta development / ventricular septum development / low-density lipoprotein particle receptor binding / hemoglobin binding / forebrain development / amyloid-beta clearance / hormone binding / vagina development / outflow tract morphogenesis / brush border / positive regulation of endocytosis / endocytic vesicle / animal organ regeneration / negative regulation of BMP signaling pathway / response to X-ray / response to retinoic acid / regulation of protein-containing complex assembly / axonal growth cone / clathrin-coated pit / receptor-mediated endocytosis / endosome lumen / nuclear receptor binding / neural tube closure / PDZ domain binding / kidney development / phosphatidylinositol 3-kinase/protein kinase B signal transduction / brush border membrane / sensory perception of sound / cellular response to growth factor stimulus / SH3 domain binding / histone deacetylase binding / male gonad development / endocytosis / apical part of cell / protein transport / protein-folding chaperone binding / heart development / regulation of gene expression / gene expression / cytoskeleton / cell population proliferation / receptor complex / endosome / apical plasma membrane / response to xenobiotic stimulus / axon / external side of plasma membrane / dendrite / calcium ion binding / ubiquitin protein ligase binding / protein kinase binding / negative regulation of apoptotic process / protein-containing complex binding / cell surface / endoplasmic reticulum / Golgi apparatus / protein-containing complex / extracellular space / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
: / LRP2-like, EGF-like domain / Complement Clr-like EGF domain / Complement Clr-like EGF-like / : / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A ...: / LRP2-like, EGF-like domain / Complement Clr-like EGF domain / Complement Clr-like EGF-like / : / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / : / Calcium-binding EGF domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Ankyrin repeat-containing domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Ankyrin repeat / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Low-density lipoprotein receptor-related protein 2 / Ankyrin repeat family A protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsLam, R. / Xu, C. / Bian, C.B. / Kania, J. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Sci.Signal. / Year: 2012
Title: Sequence-Specific Recognition of a PxLPxI/L Motif by an Ankyrin Repeat Tumbler Lock.
Authors: Xu, C. / Jin, J. / Bian, C. / Lam, R. / Tian, R. / Weist, R. / You, L. / Nie, J. / Bochkarev, A. / Tempel, W. / Tan, C.S. / Wasney, G.A. / Vedadi, M. / Gish, G.D. / Arrowsmith, C.H. / ...Authors: Xu, C. / Jin, J. / Bian, C. / Lam, R. / Tian, R. / Weist, R. / You, L. / Nie, J. / Bochkarev, A. / Tempel, W. / Tan, C.S. / Wasney, G.A. / Vedadi, M. / Gish, G.D. / Arrowsmith, C.H. / Pawson, T. / Yang, X.J. / Min, J.
History
DepositionDec 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ankyrin repeat family A protein 2
B: Low-density lipoprotein receptor-related protein 2


Theoretical massNumber of molelcules
Total (without water)22,3702
Polymers22,3702
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-10 kcal/mol
Surface area8350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.266, 49.569, 41.059
Angle α, β, γ (deg.)90.000, 97.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ankyrin repeat family A protein 2 / RFXANK-like protein 2


Mass: 20257.834 Da / Num. of mol.: 1 / Fragment: UNP residues 148-313 (ANK repeats)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANKRA, ANKRA2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-pRARE2 / References: UniProt: Q9H9E1
#2: Protein/peptide Low-density lipoprotein receptor-related protein 2 / LRP-2 / Glycoprotein 330 / gp330 / Megalin


Mass: 2112.515 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in rat LRP2/megalin.
Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P98158
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 1.73 Å3/Da / Density % sol: 28.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes, pH 7.5, 0.2M ammonium acetate, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97941 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2010
Details: Rosenbaum-Rock high-resolution double-crystal monochromator
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 11646 / % possible obs: 95.1 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.096 / Χ2: 0.996 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.89-1.973.90.2639270.863176.8
1.97-2.054.10.22110471.035185.5
2.05-2.144.20.21111241.018192.5
2.14-2.254.30.19411931.015198.1
2.25-2.394.50.16912121.049199.8
2.39-2.584.50.14412260.9541100
2.58-2.844.50.12611961.0241100
2.84-3.254.50.10712350.9791100
3.25-4.094.40.09212281.025199.7
4.09-504.20.07112580.962198.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.15 Å37.94 Å
Translation2.15 Å37.94 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
EPICS-basedbeamline controldata collection
dataacquisition systemsdata collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SO8

3so8


Resolution: 1.89→40.71 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.297 / WRfactor Rwork: 0.254 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.297 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2693 557 4.8 %RANDOM
Rwork0.2266 ---
obs0.2287 11633 94.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 63.24 Å2 / Biso mean: 35.2059 Å2 / Biso min: 18.86 Å2
Baniso -1Baniso -2Baniso -3
1-5.79 Å20 Å2-1.18 Å2
2---3.15 Å20 Å2
3----2.95 Å2
Refinement stepCycle: LAST / Resolution: 1.89→40.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 0 21 1294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211304
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9791778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4365171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.91325.76952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65115215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.259153
X-RAY DIFFRACTIONr_chiral_restr0.0750.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021973
X-RAY DIFFRACTIONr_mcbond_it0.5791.5843
X-RAY DIFFRACTIONr_mcangle_it1.14221348
X-RAY DIFFRACTIONr_scbond_it1.9913461
X-RAY DIFFRACTIONr_scangle_it3.3544.5428
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.89-1.9370.262210.29752690460.509
1.937-1.990.335290.27870489082.36
1.99-2.0480.278430.26371585388.863
2.048-2.1110.36400.26573583892.482
2.111-2.180.305400.26674580897.153
2.18-2.2560.297420.2773378698.601
2.256-2.3410.249250.26172174799.866
2.341-2.4360.331300.279702732100
2.436-2.5440.319370.245660697100
2.544-2.6680.384260.264640666100
2.668-2.8110.262300.279611641100
2.811-2.9810.293370.23579616100
2.981-3.1850.28220.206535557100
3.185-3.4390.248350.214500535100
3.439-3.7640.195160.18946948699.794
3.764-4.2040.205260.18441444499.099
4.204-4.8460.322160.17937640098
4.846-5.9140.253190.216318337100
5.914-8.2770.216200.21245265100
8.277-40.7060.35130.21714815796.178
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)
10.48630.03460.65310.69620.1721.3041-0.1466-0.0378-0.10110.03090.1328-0.0241-0.08150.00450.01380.09240.04140.03540.22480.01220.2001-10.80090.675113.3245
26.3773-2.52587.47881.2061-1.189524.48780.13340.42060.6903-0.099-0.154-0.3941-0.38610.55910.02050.16020.00610.04910.20890.06830.2915-4.73413.70880.5347
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A151 - 308
2X-RAY DIFFRACTION2B9 - 19

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