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- PDB-3lbs: Crystal structure of the cytoplasmic tail of (pro)renin receptor ... -

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Basic information

Entry
Database: PDB / ID: 3lbs
TitleCrystal structure of the cytoplasmic tail of (pro)renin receptor as a MBP fusion (Maltose-bound form)
ComponentsMaltose-binding periplasmic protein, Renin receptor
KeywordsTRANSPORT PROTEIN / renin receptor / prorenin receptor / ATP6AP2 / cytoplasmic tail / Maltose binding protein fusion / Sugar transport / Transport
Function / homology
Function and homology information


eye pigmentation / central nervous system maturation / intracellular pH reduction / rostrocaudal neural tube patterning / positive regulation of transforming growth factor beta1 production / synaptic vesicle lumen acidification / Golgi lumen acidification / lysosomal lumen acidification / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V0 domain ...eye pigmentation / central nervous system maturation / intracellular pH reduction / rostrocaudal neural tube patterning / positive regulation of transforming growth factor beta1 production / synaptic vesicle lumen acidification / Golgi lumen acidification / lysosomal lumen acidification / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / head morphogenesis / vacuolar acidification / dendritic spine membrane / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / autophagosome membrane / regulation of MAPK cascade / tertiary granule membrane / ficolin-1-rich granule membrane / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / positive regulation of Wnt signaling pathway / carbohydrate transport / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / proton transmembrane transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / synaptic vesicle membrane / positive regulation of canonical Wnt signaling pathway / signaling receptor activity / outer membrane-bounded periplasmic space / postsynaptic membrane / lysosome / periplasmic space / endosome membrane / lysosomal membrane / axon / external side of plasma membrane / Golgi membrane / DNA damage response / Neutrophil degranulation / endoplasmic reticulum membrane / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Renin receptor-like / Renin receptor-like protein / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Renin receptor / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsZhang, Y. / Garavito, R.M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Structural analysis of the intracellular domain of (pro)renin receptor fused to maltose-binding protein.
Authors: Zhang, Y. / Gao, X. / Michael Garavito, R.
History
DepositionJan 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Maltose-binding periplasmic protein, Renin receptor
B: Maltose-binding periplasmic protein, Renin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5084
Polymers84,8242
Non-polymers6852
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-10 kcal/mol
Surface area29820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.949, 96.784, 191.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsDimer

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Components

#1: Protein Maltose-binding periplasmic protein, Renin receptor / MMBP / Maltodextrin-binding protein / Renin/prorenin receptor / ATPase H(+)-transporting lysosomal ...MMBP / Maltodextrin-binding protein / Renin/prorenin receptor / ATPase H(+)-transporting lysosomal accessory protein 2 / ATPase H(+)-transporting lysosomal-interacting protein 2 / Vacuolar ATP synthase membrane sector-associated protein M8-9 / V-ATPase M8.9 subunit / ATP6M8-9 / N14F / ER-localized type I transmembrane adaptor / Embryonic liver differentiation factor 10


Mass: 42411.875 Da / Num. of mol.: 2
Fragment: Maltose-binding periplasmic protein, residues 29-390, Renin receptor, residues 332-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: b4034, JW3994, malE, ATP6AP2, ATP6IP2, CAPER, ELDF10, HT028, MSTP009, PSEC0072
Plasmid: pLW01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AEX9, UniProt: O75787
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5
Details: 28% PEG4000, 0.2M Magnesium Chloride, 0.1 M Cacodylate, pH 6.5, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.996→35.601 Å / Num. all: 54212 / Num. obs: 51668 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 29.41 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.48
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4753 / % possible all: 89.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ANF

1anf


Resolution: 2.15→35.6 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.9 / SU B: 6.687 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.29 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27768 1331 3.2 %RANDOM
Rwork0.21227 ---
all0.2207 41847 --
obs0.21439 40617 96.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.696 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2--0.46 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.15→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5814 0 46 306 6166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226004
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.9738157
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7975746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19725.802262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.68115989
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3261512
X-RAY DIFFRACTIONr_chiral_restr0.1170.2891
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214554
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9631.53722
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66325963
X-RAY DIFFRACTIONr_scbond_it2.76732280
X-RAY DIFFRACTIONr_scangle_it4.214.52194
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 90 -
Rwork0.262 3033 -
obs--97.23 %

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