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- PDB-3lc8: Crystal structure of the cytoplasmic tail of (pro)renin receptor ... -

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Basic information

Entry
Database: PDB / ID: 3lc8
TitleCrystal structure of the cytoplasmic tail of (pro)renin receptor as a MBP fusion (Maltose-free 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


intracellular pH reduction / eye pigmentation / central nervous system maturation / rostrocaudal neural tube patterning / positive regulation of transforming growth factor beta1 production / Golgi lumen acidification / synaptic vesicle lumen acidification / clathrin-coated vesicle membrane / lysosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain ...intracellular pH reduction / eye pigmentation / central nervous system maturation / rostrocaudal neural tube patterning / positive regulation of transforming growth factor beta1 production / Golgi lumen acidification / synaptic vesicle lumen acidification / clathrin-coated vesicle membrane / lysosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / head morphogenesis / vacuolar acidification / dendritic spine membrane / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / tertiary granule membrane / regulation of MAPK cascade / autophagosome membrane / ficolin-1-rich granule membrane / carbohydrate transmembrane transporter activity / positive regulation of Wnt signaling pathway / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / ATP-binding cassette (ABC) transporter complex / proton transmembrane transport / cell chemotaxis / synaptic vesicle membrane / positive regulation of canonical Wnt signaling pathway / signaling receptor activity / outer membrane-bounded periplasmic space / postsynaptic membrane / periplasmic space / lysosome / endosome membrane / Golgi membrane / axon / external side of plasma membrane / lysosomal 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
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 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 10, 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 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)85,5138
Polymers84,8242
Non-polymers6896
Water9,710539
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-7 kcal/mol
Surface area32090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.780, 112.700, 175.110
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 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: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5
Details: 20% PEG 4000, 0.2M Magnesium Chloride, 0.1M Tris, pH 8.5, 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: Jan 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→29.745 Å / Num. all: 65038 / Num. obs: 63627 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 26.64 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 15.15
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 4 / Num. unique all: 6275 / % possible all: 98.9

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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 1JW4

1jw4


Resolution: 2→29.745 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.897 / SU B: 3.836 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.167 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25741 1932 3 %RANDOM
Rwork0.19535 ---
obs0.19732 61694 97.88 %-
all-65038 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.125 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→29.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5791 0 45 539 6375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0225970
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.9698094
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78925.83259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4815983
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9571511
X-RAY DIFFRACTIONr_chiral_restr0.1330.2869
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214533
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_it1.211.53712
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.00225946
X-RAY DIFFRACTIONr_scbond_it3.12532258
X-RAY DIFFRACTIONr_scangle_it4.8014.52148
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 150 -
Rwork0.209 4496 -
obs--98.89 %

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