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- PDB-3v2x: Crystal Structure of the Peptide Bound Complex of the Ankyrin Rep... -

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Basic information

Entry
Database: PDB / ID: 3v2x
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 / diol metabolic process / positive regulation of oligodendrocyte progenitor proliferation / pulmonary artery morphogenesis / secondary heart field specification / Retinoid metabolism and transport / folate import across plasma membrane / metanephric proximal tubule development ...endocytic hemoglobin import into cell / chemoattraction of axon / Transport of RCbl within the body / diol metabolic process / positive regulation of oligodendrocyte progenitor proliferation / pulmonary artery morphogenesis / secondary heart field specification / Retinoid metabolism and transport / folate import across plasma membrane / metanephric proximal tubule development / Vitamin D (calciferol) metabolism / ventricular compact myocardium morphogenesis / response to leptin / protein transporter activity / positive regulation of lipoprotein transport / metal ion transport / negative regulation of endopeptidase activity / hormone binding / vitamin D metabolic process / cranial skeletal system development / Cargo recognition for clathrin-mediated endocytosis / neuron projection arborization / Clathrin-mediated endocytosis / coronary artery morphogenesis / transcytosis / insulin-like growth factor I binding / outflow tract septum morphogenesis / protein import / response to vitamin D / coronary vasculature development / cargo receptor activity / aorta development / ventricular septum development / endosomal transport / positive regulation of neurogenesis / low-density lipoprotein particle receptor binding / hemoglobin binding / vagina development / positive regulation of endocytosis / amyloid-beta clearance / outflow tract morphogenesis / brush border / negative regulation of BMP signaling pathway / endocytic vesicle / response to X-ray / animal organ regeneration / regulation of protein-containing complex assembly / response to retinoic acid / axonal growth cone / forebrain development / clathrin-coated pit / receptor-mediated endocytosis / endosome lumen / nuclear receptor binding / kidney development / PDZ domain binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / neural tube closure / sensory perception of sound / brush border membrane / cellular response to growth factor stimulus / SH3 domain binding / histone deacetylase binding / endocytosis / male gonad development / 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 / ubiquitin protein ligase binding / calcium ion binding / protein-containing complex binding / negative regulation of apoptotic process / protein kinase 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 / Low-density lipoprotein (LDL) receptor class A, conserved site ...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 / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / : / Calcium-binding EGF domain / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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)19,3642
Polymers19,3642
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-13 kcal/mol
Surface area9070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.962, 32.750, 45.314
Angle α, β, γ (deg.)78.510, 75.170, 65.950
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 18171.551 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: 1192.510 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.: 78 / 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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris, pH 6.5, 0.2M NaCl, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 7, 2010 / Details: VariMax HF optics
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 11884 / % possible obs: 92.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.043 / Χ2: 1.042 / Net I/σ(I): 18
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.892.70.1716040.62169.1
1.89-1.943.10.1797070.705182.1
1.94-1.993.60.1617840.953189.8
1.99-2.053.80.1457941.105192.2
2.05-2.123.90.1257771.143192
2.12-2.193.90.1177991.09193.7
2.19-2.283.90.0968171.064192.9
2.28-2.393.90.0818011.118194.5
2.39-2.513.90.0728301.094194.4
2.51-2.673.90.0587941.159194.5
2.67-2.873.90.0458230.973196.1
2.87-3.163.90.0378290.956196.4
3.16-3.623.90.038291.211196.7
3.62-4.563.90.0298481.075198
4.56-503.80.0338480.992198.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.07 Å21.78 Å
Translation2.07 Å21.78 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
JDirectordata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SO8

3so8


Resolution: 1.85→43.55 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.231 / WRfactor Rwork: 0.189 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 7.539 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 575 4.8 %RANDOM
Rwork0.1807 ---
obs0.1823 11879 91.83 %-
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: 59.74 Å2 / Biso mean: 30.7352 Å2 / Biso min: 15.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å2-0.16 Å20.18 Å2
2--1.12 Å2-0.11 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.85→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1340 0 0 78 1418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221372
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9821865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5795177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.0625.71456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60415235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.496154
X-RAY DIFFRACTIONr_chiral_restr0.0760.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211018
X-RAY DIFFRACTIONr_mcbond_it0.611.5879
X-RAY DIFFRACTIONr_mcangle_it1.18621405
X-RAY DIFFRACTIONr_scbond_it2.1243493
X-RAY DIFFRACTIONr_scangle_it3.4264.5459
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 (%)
1.85-1.8970.369300.23763296968.318
1.897-1.9490.327380.21471490982.728
1.949-2.0050.293350.21381193890.192
2.005-2.0670.241390.21776386992.29
2.067-2.1350.273460.20175086891.705
2.135-2.2090.218430.18469779193.552
2.209-2.2930.206340.17973381793.88
2.293-2.3860.196390.18867775894.459
2.386-2.4920.279300.18667274793.976
2.492-2.6130.2290.19662168594.891
2.613-2.7540.334160.19262867395.691
2.754-2.920.231340.22156462495.833
2.92-3.1210.254320.19654459696.644
3.121-3.3690.216300.17950555396.745
3.369-3.6890.205220.16447651297.266
3.689-4.120.168310.15142146497.414
4.12-4.7510.152280.13836540098.25
4.751-5.8010.17250.1833434299.123
5.801-8.1320.182100.1626027199.631
8.132-43.550.05840.1413715094
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)
10.20770.05930.0120.856-0.41170.58670.00470.0294-0.01250.0116-0.01690.0202-0.0282-0.03530.01220.01470.00660.00220.0223-0.00840.0146-0.5658-0.20410.9831
20.3083-1.96370.96914.7651-1.12462.92490.0277-0.0165-0.4071-0.18940.37050.8174-0.065-0.064-0.39820.0148-0.0732-0.01120.1918-0.04180.1353-7.2563-5.5489-8.6047
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A147 - 312
2X-RAY DIFFRACTION2B1 - 11

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