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- PDB-1ytv: Maltose-binding protein fusion to a C-terminal fragment of the V1... -

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Basic information

Entry
Database: PDB / ID: 1ytv
TitleMaltose-binding protein fusion to a C-terminal fragment of the V1a vasopressin receptor
Components
  • Maltose-binding periplasmic protein
  • Vasopressin V1a receptor
KeywordsSUGAR BINDING PROTEIN / HORMONE RECEPTOR / vasopressin / receptor / GPCR / fusion protein / maltose-binding protein
Function / homology
Function and homology information


Defective AVP does not bind AVPR1A,B and causes neurohypophyseal diabetes insipidus (NDI) / maternal aggressive behavior / cellular response to water deprivation / V1A vasopressin receptor binding / penile erection / negative regulation of transmission of nerve impulse / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / positive regulation of renal sodium excretion / vasopressin receptor activity ...Defective AVP does not bind AVPR1A,B and causes neurohypophyseal diabetes insipidus (NDI) / maternal aggressive behavior / cellular response to water deprivation / V1A vasopressin receptor binding / penile erection / negative regulation of transmission of nerve impulse / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / positive regulation of renal sodium excretion / vasopressin receptor activity / negative regulation of female receptivity / myotube differentiation / sperm ejaculation / telencephalon development / positive regulation of systemic arterial blood pressure / grooming behavior / positive regulation of prostaglandin biosynthetic process / maternal behavior / positive regulation of glutamate secretion / blood circulation / positive regulation of heart rate / response to corticosterone / detection of maltose stimulus / maltose transport complex / plasma membrane => GO:0005886 / carbohydrate transport / peptide hormone binding / social behavior / : / transport across blood-brain barrier / carbohydrate transmembrane transporter activity / maltose binding / endocytic vesicle / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / positive regulation of vasoconstriction / ATP-binding cassette (ABC) transporter complex / positive regulation of cellular pH reduction / cell chemotaxis / generation of precursor metabolites and energy / G protein-coupled receptor activity / calcium-mediated signaling / protein kinase C binding / peptide binding / positive regulation of cytosolic calcium ion concentration / outer membrane-bounded periplasmic space / positive regulation of cell growth / G alpha (q) signalling events / periplasmic space / endosome / G protein-coupled receptor signaling pathway / DNA damage response / positive regulation of cell population proliferation / membrane / plasma membrane
Similarity search - Function
Vasopressin V1A receptor / Vasopressin V1 receptor, C-terminal / Vasopressin V1 receptor, C-terminal / DUF1856 / Vasopressin receptor / 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 ...Vasopressin V1A receptor / Vasopressin V1 receptor, C-terminal / Vasopressin V1 receptor, C-terminal / DUF1856 / Vasopressin receptor / 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 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein / Vasopressin V1a receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAdikesavan, N.V. / Mahmood, S.S. / Stanley, S. / Xu, Z. / Wu, N. / Thibonnier, M. / Shoham, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2005
Title: A C-terminal segment of the V1R vasopressin receptor is unstructured in the crystal structure of its chimera with the maltose-binding protein.
Authors: Adikesavan, N.V. / Mahmood, S.S. / Stanley, N. / Xu, Z. / Wu, N. / Thibonnier, M. / Shoham, M.
History
DepositionFeb 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / 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 / _atom_site.type_symbol / _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 / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 21, 2022Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein
M: Vasopressin V1a receptor
B: Maltose-binding periplasmic protein
N: Vasopressin V1a receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3146
Polymers99,6304
Non-polymers6852
Water11,548641
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.102, 66.557, 115.723
Angle α, β, γ (deg.)90.00, 95.99, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsThe second molecule in the asymmetric unit is related by a two-fold axis

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Components

#1: Protein Maltose-binding periplasmic protein / Maltodextrin-binding protein / MMBP / maltose transport protein / chemotaxis (ABC superfamily / peri_bind)


Mass: 40252.520 Da / Num. of mol.: 2 / Fragment: c-terminal residues 27-392
Source method: isolated from a genetically manipulated source
Details: ONE FUSED PROTEIN IS MADE OF CHAINS A+M, THE OTHER B+N
Source: (gene. exp.) Escherichia coli (E. coli) / Description: expressed with second entity as one protein / Gene: malE / Plasmid: PSV282 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02928, UniProt: P0AEX9*PLUS
#2: Protein Vasopressin V1a receptor / V1aR / Vascular/hepatic-type arginine vasopressin receptor / Antidiuretic hormone receptor 1a / ...V1aR / Vascular/hepatic-type arginine vasopressin receptor / Antidiuretic hormone receptor 1a / AVPR V1a / arginine vasopressin receptor 1A


Mass: 9562.329 Da / Num. of mol.: 2 / Fragment: linker + residues 362-418
Source method: isolated from a genetically manipulated source
Details: ONE FUSED PROTEIN IS MADE OF CHAINS A+M, THE OTHER B+N
Source: (gene. exp.) Homo sapiens (human) / Description: expressed with first entity as one protein / Gene: AVPR1A / Plasmid: PSV282 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P37288
#3: 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
[][D-1-deoxy-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / 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: 2.2 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Ammonium sulfate, 25%(v/v)PEG 400 and 25%(v/v) glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97934 Å
DetectorDetector: CCD / Date: Nov 18, 2003 / Details: Mirrors
RadiationMonochromator: Si-111, Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.8→34.43 Å / Num. all: 71204 / Observed criterion σ(F): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 19.1 Å2 / Limit h max: 28 / Limit h min: -28 / Limit k max: 36 / Limit k min: -28 / Limit l max: 64 / Limit l min: 0 / Observed criterion F max: 1630376.1 / Observed criterion F min: 15.8 / Rmerge(I) obs: 0.076 / Net I/σ(I): 16.8
Reflection shellResolution: 1.8→1.86 Å

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.362 / Packing: 0.299
Highest resolutionLowest resolutionReflection percentσ(F)
Translation4 Å15 Å99.7 0

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A7L

1a7l


Resolution: 1.8→34.43 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / σ(I): 0 / Details: throughout
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3609 5.1 %random
Rwork0.199 ---
all0.1955 71534 --
obs-71204 99.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 52.8902 Å2 / ksol: 0.38898 e/Å3
Displacement parametersBiso max: 91.67 Å2 / Biso mean: 22.99 Å2 / Biso min: 8.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20.18 Å2
2--5.17 Å20 Å2
3----4.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.8→34.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5760 0 44 641 6445
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg21.7
X-RAY DIFFRACTIONx_torsion_impr_deg0.84
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.870.2773364.80.2766150.0157151695197.2
1.87-1.940.2683615.10.23467060.0147084706799.7
1.94-2.030.2283294.60.20868130.0137154714299.8
2.03-2.140.2523494.90.20467910.0147160714099.7
2.14-2.270.2344065.70.19667020.0127121710899.8
2.27-2.440.2253474.90.18967800.0127139712799.8
2.44-2.690.2454095.70.19967480.0127164715799.9
2.69-3.080.2343625.10.20867660.0127139712899.8
3.08-3.880.18635950.18368450.017210720499.9
3.88-34.430.2133514.90.19268290.0117311718098.2

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