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- PDB-3n94: Crystal structure of human pituitary adenylate cyclase 1 Receptor... -

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Entry
Database: PDB / ID: 3n94
TitleCrystal structure of human pituitary adenylate cyclase 1 Receptor-short N-terminal extracellular domain
ComponentsFusion protein of Maltose-binding periplasmic protein and pituitary adenylate cyclase 1 Receptor-short
KeywordsMEMBRANE RECEPTOR / G-protein coupled receptor / MBP fusion protein / peptide hormone receptor
Function / homology
Function and homology information


small GTPase binding => GO:0031267 / development of primary female sexual characteristics / vasoactive intestinal polypeptide receptor activity / : / response to xenobiotic stimulus => GO:0009410 / positive regulation of cAMP-mediated signaling / NGF-independant TRKA activation / neuropeptide binding / G protein-coupled peptide receptor activity / positive regulation of small GTPase mediated signal transduction ...small GTPase binding => GO:0031267 / development of primary female sexual characteristics / vasoactive intestinal polypeptide receptor activity / : / response to xenobiotic stimulus => GO:0009410 / positive regulation of cAMP-mediated signaling / NGF-independant TRKA activation / neuropeptide binding / G protein-coupled peptide receptor activity / positive regulation of small GTPase mediated signal transduction / positive regulation of inositol phosphate biosynthetic process / positive regulation of calcium ion transport into cytosol / detection of maltose stimulus / maltose transport complex / plasma membrane => GO:0005886 / carbohydrate transport / peptide hormone binding / adenylate cyclase binding / : / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / bicellular tight junction / multicellular organismal response to stress / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / rough endoplasmic reticulum / ATP-binding cassette (ABC) transporter complex / cAMP-mediated signaling / cell chemotaxis / caveola / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Glucagon-type ligand receptors / ADORA2B mediated anti-inflammatory cytokines production / response to estradiol / signaling receptor activity / outer membrane-bounded periplasmic space / G alpha (s) signalling events / spermatogenesis / response to ethanol / periplasmic space / cell surface receptor signaling pathway / cell differentiation / receptor complex / endosome / neuron projection / G protein-coupled receptor signaling pathway / intracellular membrane-bounded organelle / DNA damage response / cell surface / membrane / plasma membrane
Similarity search - Function
GPCR, family 2, pituitary adenylate cyclase activating polypeptide type 1 receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like ...GPCR, family 2, pituitary adenylate cyclase activating polypeptide type 1 receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / 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 / Pituitary adenylate cyclase-activating polypeptide type I receptor / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKumar, S. / Pioszak, A.A. / Swaminathan, K. / Xu, H.E.
CitationJournal: Plos One / Year: 2011
Title: Crystal Structure of the PAC1R Extracellular Domain Unifies a Consensus Fold for Hormone Recognition by Class B G-Protein Coupled Receptors.
Authors: Kumar, S. / Pioszak, A. / Zhang, C. / Swaminathan, K. / Xu, H.E.
History
DepositionMay 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_conn_type / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_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

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Assembly

Deposited unit
A: Fusion protein of Maltose-binding periplasmic protein and pituitary adenylate cyclase 1 Receptor-short
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1763
Polymers52,7371
Non-polymers4382
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.987, 92.151, 105.418
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 Fusion protein of Maltose-binding periplasmic protein and pituitary adenylate cyclase 1 Receptor-short / MMBP / Maltodextrin-binding protein / Pituitary adenylate Cyclase 1 Receptor


Mass: 52737.465 Da / Num. of mol.: 1 / Fragment: UNP 26-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: malE, b4034, JW3994, ADCYAP1R1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: B8ZZK3
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS ENTRY IS A FUSION BETWEEN MALTOSE BINDING PROTEIN (MBP) AND PITUITARY ADENYLATE CYCLASE 1 ...THIS ENTRY IS A FUSION BETWEEN MALTOSE BINDING PROTEIN (MBP) AND PITUITARY ADENYLATE CYCLASE 1 RECEPTOR WITH A SHORT LINKER IN BETWEEN

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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: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25.5% PEG 4000, 15% Glycerol, 170mM Ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.8→69.38 Å / Num. obs: 42645 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 13.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 28.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.968 / Mean I/σ(I) obs: 2.04 / Num. unique all: 4174 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C4M

3c4m


Resolution: 1.8→69.38 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.935 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.129 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2148 5 %RANDOM
Rwork0.176 ---
obs0.178 42582 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 92.37 Å2 / Biso mean: 34.044 Å2 / Biso min: 13.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2---0.36 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.8→69.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3619 0 28 263 3910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223788
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.9645157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9245479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19725.756172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95715625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.626159
X-RAY DIFFRACTIONr_chiral_restr0.1290.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212906
X-RAY DIFFRACTIONr_mcbond_it0.9871.52342
X-RAY DIFFRACTIONr_mcangle_it1.73623760
X-RAY DIFFRACTIONr_scbond_it3.14931446
X-RAY DIFFRACTIONr_scangle_it4.964.51390
LS refinement shellResolution: 1.8→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 153 -
Rwork0.293 2933 -
all-3086 -
obs--98.69 %
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)
11.23490.10260.24251.97480.6240.91070.0113-0.1369-0.1150.25360.0028-0.02680.14090.0137-0.01410.0612-0.01120.00720.06570.00140.01575.8013-0.6033-14.8258
21.87090.2421-0.63780.6139-0.97382.63450.0559-0.1053-0.05530.0631-0.0388-0.0493-0.07370.1242-0.01710.0427-0.00290.0050.0693-0.00890.0411.963516.68918.0254
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-346 - 22
2X-RAY DIFFRACTION1A5044
3X-RAY DIFFRACTION2A23 - 119

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