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- PDB-2x57: Crystal structure of the extracellular domain of human Vasoactive... -

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Basic information

Entry
Database: PDB / ID: 2x57
TitleCrystal structure of the extracellular domain of human Vasoactive intestinal polypeptide receptor 2
ComponentsVASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 2
KeywordsIMMUNE SYSTEM / G-PROTEIN COUPLED RECEPTOR / CIRCADIAN RHYTHM / MALE REPRODUCTION / HORMONE BINDING / GROWTH / RECEPTOR / TRANSDUCER / CLASS B GPCR
Function / homology
Function and homology information


vasoactive intestinal polypeptide receptor activity / G protein-coupled peptide receptor activity / peptide hormone binding / G protein-coupled receptor activity / negative regulation of smooth muscle cell proliferation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Glucagon-type ligand receptors / cell-cell signaling / G alpha (s) signalling events / cell surface receptor signaling pathway ...vasoactive intestinal polypeptide receptor activity / G protein-coupled peptide receptor activity / peptide hormone binding / G protein-coupled receptor activity / negative regulation of smooth muscle cell proliferation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Glucagon-type ligand receptors / cell-cell signaling / G alpha (s) signalling events / cell surface receptor signaling pathway / signal transduction / plasma membrane
Similarity search - Function
GPCR, family 2, vasoactive intestinal peptide receptor 2 / : / GPCR, family 2, vasoactive intestinal peptide 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, vasoactive intestinal peptide receptor 2 / : / GPCR, family 2, vasoactive intestinal peptide 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.
Similarity search - Domain/homology
Vasoactive intestinal polypeptide receptor 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsPike, A.C.W. / Barr, A.J. / Quigley, A. / Burgess Brown, N. / de Riso, A. / Bullock, A. / Berridge, G. / Muniz, J.R.C. / Chaikaud, A. / Vollmar, M. ...Pike, A.C.W. / Barr, A.J. / Quigley, A. / Burgess Brown, N. / de Riso, A. / Bullock, A. / Berridge, G. / Muniz, J.R.C. / Chaikaud, A. / Vollmar, M. / Krojer, T. / Ugochukwu, E. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Carpenter, E.P.
CitationJournal: To be Published
Title: Crystal Structure of the Extracellular Domain of Human Vasoactive Intestinal Polypeptide Receptor 2
Authors: Pike, A.C.W. / Barr, A.J. / Quigley, A. / Burgess Brown, N. / De Riso, A. / Bullock, A. / Berridge, G. / Muniz, J.R.C. / Chaikaud, A. / Vollmar, M. / Krojer, T. / Ugochukwu, E. / von Delft, ...Authors: Pike, A.C.W. / Barr, A.J. / Quigley, A. / Burgess Brown, N. / De Riso, A. / Bullock, A. / Berridge, G. / Muniz, J.R.C. / Chaikaud, A. / Vollmar, M. / Krojer, T. / Ugochukwu, E. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Carpenter, E.P.
History
DepositionFeb 5, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 2
B: VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 2
C: VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)39,7933
Polymers39,7933
Non-polymers00
Water2,468137
1
A: VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 2
B: VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 2
C: VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 2

A: VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 2
B: VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 2
C: VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)79,5856
Polymers79,5856
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area15470 Å2
ΔGint-69.6 kcal/mol
Surface area27190 Å2
MethodPISA
2
A: VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)13,2641
Polymers13,2641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)13,2641
Polymers13,2641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)13,2641
Polymers13,2641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.700, 99.700, 104.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
13A
23B
33C
14A
24B
34C
15A
25C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A16 - 20
2115B16 - 20
3115C16 - 20
1215A22 - 24
2215B22 - 24
3215C22 - 24
1125A25 - 28
2125B25 - 28
3125C25 - 28
1221A29 - 32
2221B29 - 32
3221C29 - 32
1321A34 - 44
2321B34 - 44
3321C34 - 44
1426A45 - 50
2426B45 - 50
3426C45 - 50
1521A51 - 56
2521B51 - 56
3521C51 - 56
1626A58 - 59
2626B58 - 59
3626C58 - 59
1724A60 - 65
2724B60 - 65
3724C60 - 65
1131A68 - 76
2131B68 - 76
3131C68 - 76
1231A89 - 90
2231B89 - 90
3231C89 - 90
1331A92 - 93
2331B92 - 93
3331C92 - 93
1142A94 - 95
2142B94 - 95
3142C94 - 95
1244A97
2244B97
3244C97
1152A98 - 111
2152C98 - 111

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 2 / PITUITARY ADENYLATE CYCLASE-ACTIVATING POLYPEPTIDE TYPE III RECEPTOR / PACAP TYPE III RECEPTOR / ...PITUITARY ADENYLATE CYCLASE-ACTIVATING POLYPEPTIDE TYPE III RECEPTOR / PACAP TYPE III RECEPTOR / HELODERMIN-PREFERRING VIP RECEPTOR / PACAP-R-3


Mass: 13264.222 Da / Num. of mol.: 3 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 26-118
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: P41587
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 3.18 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 4.2 / Details: 40% PEG300 0.1M CITRATE PHOSPHATE PH4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9809, 0.9799
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98091
20.97991
ReflectionResolution: 2.1→58.41 Å / Num. obs: 31377 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.793 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.148
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23477 1577 5 %RANDOM
Rwork0.20707 ---
obs0.20844 29739 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.198 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 0 137 2567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222514
X-RAY DIFFRACTIONr_bond_other_d0.0010.021679
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.9243421
X-RAY DIFFRACTIONr_angle_other_deg1.3373.0094073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9435308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.85425.161124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41815394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.382159
X-RAY DIFFRACTIONr_chiral_restr0.0910.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212832
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02512
X-RAY DIFFRACTIONr_nbd_refined0.2290.2545
X-RAY DIFFRACTIONr_nbd_other0.1820.21586
X-RAY DIFFRACTIONr_nbtor_refined0.1970.21263
X-RAY DIFFRACTIONr_nbtor_other0.0940.21294
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2115
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1170.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1520.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0530.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.67931548
X-RAY DIFFRACTIONr_mcbond_other1.2113625
X-RAY DIFFRACTIONr_mcangle_it5.97952507
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.5448966
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it12.09312914
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
21A277tight positional0.230.05
22B277tight positional0.230.05
23C277tight positional0.260.05
31A147tight positional0.050.05
32B147tight positional0.070.05
33C147tight positional0.050.05
41A12tight positional0.070.05
42B12tight positional0.050.05
43C12tight positional0.060.05
51A82tight positional0.050.05
52C82tight positional0.050.05
11A47medium positional0.090.5
12B47medium positional0.10.5
13C47medium positional0.110.5
21A114medium positional0.340.5
22B114medium positional0.290.5
23C114medium positional0.290.5
41A15medium positional0.240.5
42B15medium positional0.260.5
43C15medium positional0.150.5
51A104medium positional0.050.5
52C104medium positional0.050.5
11A51loose positional0.165
12B51loose positional0.135
13C51loose positional0.175
21A152loose positional0.535
22B152loose positional0.575
23C152loose positional0.615
21A277tight thermal1.360.5
22B277tight thermal1.210.5
23C277tight thermal1.230.5
31A147tight thermal0.210.5
32B147tight thermal0.270.5
33C147tight thermal0.240.5
41A12tight thermal1.40.5
42B12tight thermal1.220.5
43C12tight thermal1.410.5
51A82tight thermal0.20.5
52C82tight thermal0.20.5
11A47medium thermal1.492
12B47medium thermal1.92
13C47medium thermal1.212
21A114medium thermal1.192
22B114medium thermal1.412
23C114medium thermal1.212
41A15medium thermal1.722
42B15medium thermal1.462
43C15medium thermal1.542
51A104medium thermal0.222
52C104medium thermal0.222
11A51loose thermal1.6610
12B51loose thermal1.6210
13C51loose thermal1.3510
21A152loose thermal1.0910
22B152loose thermal1.1910
23C152loose thermal1.2210
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 117 -
Rwork0.363 2144 -
obs--99.91 %
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)
12.15280.24640.0522.12110.16725.47560.1211-0.44050.17710.26940.0489-0.0987-0.17480.0677-0.170.1218-0.0420.04690.1133-0.04840.069713.51110.4955-13.8984
21.6525-1.69590.79113.9732-1.62290.840.09210.1935-0.0137-0.3301-0.0761-0.14040.15090.0728-0.01610.1025-0.00810.01680.0434-0.01390.043117.6107-2.402-40.162
32.6213-1.2925-0.11142.86870.85250.4438-0.0272-0.1659-0.00230.11550.0948-0.47290.00330.0339-0.06760.0705-0.007-0.02260.02850.01460.18831.5291-16.9331-22.5056
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 114
2X-RAY DIFFRACTION2B10 - 114
3X-RAY DIFFRACTION3C12 - 114

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