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- PDB-3so6: Crystal structure of the LDL receptor tail in complex with autoso... -

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Basic information

Entry
Database: PDB / ID: 3so6
TitleCrystal structure of the LDL receptor tail in complex with autosomal recessive hypercholesterolemia PTB domain
Components
  • LDL receptor adaptor protein
  • Low-density lipoprotein receptor
KeywordsPROTEIN BINDING/PROTEIN TRANSPORT / PTB / endocytic adaptor / receptor / ldl / ldlr / autosomal recessive hypercholesterolemia / ARH / cholesterol / PROTEIN BINDING-PROTEIN TRANSPORT complex
Function / homology
Function and homology information


Chylomicron clearance / AP-1 adaptor complex binding / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / very-low-density lipoprotein particle receptor activity / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / negative regulation of astrocyte activation / neurofilament / positive regulation of low-density lipoprotein particle clearance ...Chylomicron clearance / AP-1 adaptor complex binding / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / very-low-density lipoprotein particle receptor activity / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / negative regulation of astrocyte activation / neurofilament / positive regulation of low-density lipoprotein particle clearance / LDL clearance / receptor-mediated endocytosis involved in cholesterol transport / negative regulation of microglial cell activation / AP-2 adaptor complex binding / PCSK9-LDLR complex / cholesterol import / negative regulation of receptor recycling / low-density lipoprotein particle clearance / clathrin heavy chain binding / low-density lipoprotein particle receptor activity / positive regulation of triglyceride biosynthetic process / negative regulation of low-density lipoprotein particle clearance / intestinal cholesterol absorption / low-density lipoprotein particle binding / Chylomicron clearance / response to caloric restriction / amyloid-beta clearance by cellular catabolic process / Cargo recognition for clathrin-mediated endocytosis / LDL clearance / Clathrin-mediated endocytosis / clathrin adaptor activity / regulation of protein binding / regulation of protein metabolic process / high-density lipoprotein particle clearance / lipoprotein catabolic process / phospholipid transport / cholesterol transport / low-density lipoprotein particle / endolysosome membrane / negative regulation of amyloid fibril formation / amyloid precursor protein metabolic process / negative regulation of protein metabolic process / artery morphogenesis / cellular response to fatty acid / regulation of cholesterol metabolic process / low-density lipoprotein particle receptor binding / clathrin binding / amyloid-beta clearance / sorting endosome / cellular response to cytokine stimulus / lipoprotein particle binding / cellular response to low-density lipoprotein particle stimulus / regulation of protein localization to plasma membrane / long-term memory / phagocytosis / signaling adaptor activity / Retinoid metabolism and transport / clathrin-coated pit / somatodendritic compartment / positive regulation of vascular associated smooth muscle cell proliferation / phosphatidylinositol-4,5-bisphosphate binding / phosphotyrosine residue binding / cholesterol metabolic process / basal plasma membrane / receptor-mediated endocytosis / cholesterol homeostasis / clathrin-coated endocytic vesicle membrane / receptor internalization / lipid metabolic process / recycling endosome / cytoplasmic side of plasma membrane / positive regulation of receptor-mediated endocytosis / positive regulation of inflammatory response / endocytosis / signaling receptor complex adaptor activity / Cargo recognition for clathrin-mediated endocytosis / late endosome / apical part of cell / Clathrin-mediated endocytosis / virus receptor activity / amyloid-beta binding / basolateral plasma membrane / protease binding / molecular adaptor activity / lysosome / early endosome / receptor complex / endosome membrane / axon / external side of plasma membrane / negative regulation of gene expression / calcium ion binding / positive regulation of gene expression / Golgi apparatus / cell surface / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / 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 ...Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / 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. / LDL-receptor class A (LDLRA) domain profile. / : / Calcium-binding EGF 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / 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. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Low density lipoprotein receptor adapter protein 1 / Low-density lipoprotein receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.37 Å
AuthorsDvir, H. / Zajonc, D.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Atomic structure of the autosomal recessive hypercholesterolemia phosphotyrosine-binding domain in complex with the LDL-receptor tail.
Authors: Dvir, H. / Shah, M. / Girardi, E. / Guo, L. / Farquhar, M.G. / Zajonc, D.M.
History
DepositionJun 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Database references
Revision 1.2May 16, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: LDL receptor adaptor protein
Q: Low-density lipoprotein receptor


Theoretical massNumber of molelcules
Total (without water)16,9082
Polymers16,9082
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-11 kcal/mol
Surface area8300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.097, 59.095, 77.083
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LDL receptor adaptor protein


Mass: 15265.929 Da / Num. of mol.: 1 / Fragment: UNP residues 43-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ldlrap1, RGD1563417_predicted, rCG_31034 / Production host: Escherichia coli (E. coli) / References: UniProt: D3ZAR1
#2: Protein/peptide Low-density lipoprotein receptor / LDL receptor


Mass: 1641.756 Da / Num. of mol.: 1 / Fragment: UNP residues 817-832 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01130
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 1.96 Å3/Da / Density % sol: 37.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES, 30% PEG6000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 4, 2010
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.37→23.563 Å / Num. all: 27539 / Num. obs: 27539 / % possible obs: 96.5 % / Observed criterion σ(F): 3.4 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rsym value: 0.054 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.37-1.444.60.3621882040620.3698.9
1.44-1.534.70.2253.31807338340.22597.9
1.53-1.644.80.1524.91697635580.15297.4
1.64-1.774.80.1126.51596633260.11296.9
1.77-1.944.80.0788.81477430540.07896.3
1.94-2.174.90.05411.81342427350.05495.7
2.17-2.54.90.05211.51201324460.05295.5
2.5-3.064.90.04512.31016520670.04595.2
3.06-4.334.90.04113.6783115960.04193.6
4.33-24.7254.70.04513.140698610.04587.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 59.98 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.27 Å
Translation2.5 Å32.27 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→23.56 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.2093 / WRfactor Rwork: 0.1533 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8877 / SU B: 2.108 / SU ML: 0.039 / SU R Cruickshank DPI: 0.0691 / SU Rfree: 0.0675 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 1437 5.2 %RANDOM
Rwork0.1515 ---
obs0.1542 27538 95.66 %-
all-28787 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.53 Å2 / Biso mean: 19.2488 Å2 / Biso min: 7.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å20 Å2
2---0.59 Å2-0 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.37→23.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 0 0 185 1353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221242
X-RAY DIFFRACTIONr_angle_refined_deg2.051.9581684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51524.28649
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17315235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.36157
X-RAY DIFFRACTIONr_chiral_restr0.160.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021901
X-RAY DIFFRACTIONr_mcbond_it2.6741.5773
X-RAY DIFFRACTIONr_mcangle_it3.88421260
X-RAY DIFFRACTIONr_scbond_it5.6483469
X-RAY DIFFRACTIONr_scangle_it7.5854.5419
X-RAY DIFFRACTIONr_rigid_bond_restr2.79131242
LS refinement shellResolution: 1.37→1.405 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 119 -
Rwork0.22 1940 -
all-2059 -
obs--98.66 %

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