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- PDB-1jk4: DES 1-6 BOVINE NEUROPHYSIN II COMPLEX WITH VASOPRESSIN -

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Basic information

Entry
Database: PDB / ID: 1jk4
TitleDES 1-6 BOVINE NEUROPHYSIN II COMPLEX WITH VASOPRESSIN
Components
  • Lys Vasopressin
  • NEUROPHYSIN 2Neurophysins
KeywordsNEUROPEPTIDE / COMPLEX (HORMONE TRANSPORT-HORMONE) / HYPOTHALAMUS
Function / homology
Function and homology information


neurohypophyseal hormone activity / V1A vasopressin receptor binding / neuropeptide hormone activity / vasoconstriction / secretory granule / extracellular space
Similarity search - Function
Neurophysin II; Chain A / Neurohypophysial hormone domain / Neurohypophysial hormone / Neurohypophysial hormone, conserved site / Neurohypophysial hormone domain superfamily / Neurohypophysial hormones, C-terminal Domain / Neurohypophysial hormones, N-terminal Domain / Neurohypophysial hormones signature. / Neurohypophysial hormones / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / : / Vasopressin-neurophysin 2-copeptin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRose, J.P. / Wang, B.-C.
Citation
Journal: Protein Sci. / Year: 2001
Title: Structures of an Unliganded Neurophysin and its Vasopressin Complex: Implications for Binding and Allosteric Mechanisms
Authors: Wu, C.K. / Hu, B. / Rose, J.P. / Liu, Z.J. / Nguyen, T.L. / Zeng, C. / Breslow, E. / Wang, B.C.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: Crystal Structure of the Neurophysin-Oxytocin Complex
Authors: Rose, J.P. / Wu, C.K. / Hsiao, C.D. / Breslow, E. / Wang, B.C.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Crystal Structure of a Bovine Neurophysin II Dipeptide Complex at 2.8 A Determined from the Single-Wavelength Anomalous Scattering Signal of an Incorporated Iodine Atom
Authors: Chen, L.Q. / Rose, J.P. / Breslow, E. / Yang, D. / Chang, W.R. / Furey Jr., W.F. / Sax, M. / Wang, B.C.
#3: Journal: Eur.J.Biochem. / Year: 1988
Title: Crystals of Modified Bovine Neurophysin II
Authors: Rose, J.P. / Yang, D. / Yoo, C.S. / Sax, M. / Breslow, E. / Wang, B.C.
#4: Journal: J.Mol.Biol. / Year: 1979
Title: Crystals of a Bovine Neurophysin II-Dipeptide Amide Complex
Authors: Yoo, C.S. / Wang, B.C. / Sax, M. / Breslow, E.
History
DepositionJul 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 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_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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _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: NEUROPHYSIN 2
B: Lys Vasopressin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6415
Polymers10,3042
Non-polymers3373
Water52229
1
A: NEUROPHYSIN 2
B: Lys Vasopressin
hetero molecules

A: NEUROPHYSIN 2
B: Lys Vasopressin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,28210
Polymers20,6084
Non-polymers6746
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Unit cell
Length a, b, c (Å)50.900, 50.900, 105.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein NEUROPHYSIN 2 / Neurophysins


Mass: 9243.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Posterior Pituitary gland / Source: (natural) Bos taurus (cattle) / References: UniProt: P01180
#2: Protein/peptide Lys Vasopressin


Mass: 1060.226 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence of the peptide is naturally found in Bos taurus (bovine).
References: GenBank: 229092, UniProt: P01180*PLUS
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 1.92 Å3/Da / Density % sol: 35.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1M sodium formate, 0.1M HEPES, 10% glycerol, 1:5 molar ratio of vasopressin to neurophysin, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: Wu, C.K., (1996) Acta Cryst., D52, 946. / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
114 mMprotein1dropin water
20.25 mg/mlsodium azide1drop
32.0 M1reservoirNaCl
40.1 MMES1reservoirpH6.5
50.05 Msodium/pootassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: YALE/MSC
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→999 Å / % possible obs: 96.2 % / Observed criterion σ(F): -3 / Rmerge(I) obs: 0.058

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Processing

Software
NameVersionClassification
MAR345data collection
X-GENdata reduction
AMoREphasing
X-PLOR3.1refinement
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BN2

2bn2


Resolution: 2.3→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.299 542 5 %RANDOM
Rwork0.234 ---
all0.234 6467 --
obs0.234 6467 92.2 %-
Displacement parametersBiso mean: 26.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms600 0 3 29 632
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d26.6
X-RAY DIFFRACTIONx_improper_angle_d1.33
Xplor fileSerial no: 1 / Param file: PARCSDX.PRO / Topol file: TOPCSDX.PRO
Refinement
*PLUS
Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.33

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