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- PDB-8t5f: De novo design of high-affinity protein binders to bioactive heli... -

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Basic information

Entry
Database: PDB / ID: 8t5f
TitleDe novo design of high-affinity protein binders to bioactive helical peptides
ComponentsParathyroid hormone
KeywordsDE NOVO PROTEIN / Alpha-helical peptides / protein design / diffusion / deep learning
Function / homology
Function and homology information


type 1 parathyroid hormone receptor binding / parathyroid hormone receptor binding / negative regulation of bone mineralization involved in bone maturation / positive regulation of osteoclast proliferation / negative regulation of apoptotic process in bone marrow cell / hormone-mediated apoptotic signaling pathway / response to parathyroid hormone / positive regulation of cell proliferation in bone marrow / magnesium ion homeostasis / positive regulation of signal transduction ...type 1 parathyroid hormone receptor binding / parathyroid hormone receptor binding / negative regulation of bone mineralization involved in bone maturation / positive regulation of osteoclast proliferation / negative regulation of apoptotic process in bone marrow cell / hormone-mediated apoptotic signaling pathway / response to parathyroid hormone / positive regulation of cell proliferation in bone marrow / magnesium ion homeostasis / positive regulation of signal transduction / macromolecule biosynthetic process / response to fibroblast growth factor / phosphate ion homeostasis / cAMP metabolic process / response to vitamin D / negative regulation of chondrocyte differentiation / Class B/2 (Secretin family receptors) / positive regulation of inositol phosphate biosynthetic process / peptide hormone receptor binding / bone mineralization / Rho protein signal transduction / : / positive regulation of glycogen biosynthetic process / positive regulation of bone mineralization / response to cadmium ion / homeostasis of number of cells within a tissue / bone resorption / skeletal system development / positive regulation of glucose import / response to lead ion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / intracellular calcium ion homeostasis / cell-cell signaling / G alpha (s) signalling events / regulation of gene expression / response to ethanol / transcription by RNA polymerase II / receptor ligand activity / response to xenobiotic stimulus / G protein-coupled receptor signaling pathway / negative regulation of gene expression / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Parathyroid hormone / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsTorres, S.V. / Leung, P.J.Y. / Bera, A.K. / Baker, D. / Kang, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2024
Title: De novo design of high-affinity binders of bioactive helical peptides.
Authors: Vazquez Torres, S. / Leung, P.J.Y. / Venkatesh, P. / Lutz, I.D. / Hink, F. / Huynh, H.H. / Becker, J. / Yeh, A.H. / Juergens, D. / Bennett, N.R. / Hoofnagle, A.N. / Huang, E. / MacCoss, M.J. ...Authors: Vazquez Torres, S. / Leung, P.J.Y. / Venkatesh, P. / Lutz, I.D. / Hink, F. / Huynh, H.H. / Becker, J. / Yeh, A.H. / Juergens, D. / Bennett, N.R. / Hoofnagle, A.N. / Huang, E. / MacCoss, M.J. / Exposit, M. / Lee, G.R. / Bera, A.K. / Kang, A. / De La Cruz, J. / Levine, P.M. / Li, X. / Lamb, M. / Gerben, S.R. / Murray, A. / Heine, P. / Korkmaz, E.N. / Nivala, J. / Stewart, L. / Watson, J.L. / Rogers, J.M. / Baker, D.
History
DepositionJun 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Parathyroid hormone
B: Parathyroid hormone
A: Parathyroid hormone


Theoretical massNumber of molelcules
Total (without water)12,3773
Polymers12,3773
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-23 kcal/mol
Surface area8800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.324, 91.324, 37.732
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11C-209-

HOH

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Components

#1: Protein/peptide Parathyroid hormone / / PTH / Parathormone / Parathyrin


Mass: 4125.778 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01270
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.4 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2 M Sodium chloride, 0.1 M Sodium acetate pH 4.5, and 1.26 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.99→40.84 Å / Num. obs: 11302 / % possible obs: 98.6 % / Redundancy: 15.1 % / Biso Wilson estimate: 46.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Net I/σ(I): 21.8
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 15.2 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 738 / CC1/2: 0.545 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIXdev_4761refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→40.84 Å / SU ML: 0.2581 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 30.6883
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2508 518 4.85 %
Rwork0.2191 10163 -
obs0.2206 10681 92.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.17 Å2
Refinement stepCycle: LAST / Resolution: 1.99→40.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms853 0 0 26 879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01867
X-RAY DIFFRACTIONf_angle_d1.04281157
X-RAY DIFFRACTIONf_chiral_restr0.058125
X-RAY DIFFRACTIONf_plane_restr0.0089145
X-RAY DIFFRACTIONf_dihedral_angle_d4.0545104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.190.33851270.25032200X-RAY DIFFRACTION83.58
2.19-2.50.28851150.24672490X-RAY DIFFRACTION92.28
2.5-3.150.28131350.2462648X-RAY DIFFRACTION96.93
3.15-40.840.22881410.20372825X-RAY DIFFRACTION98.28
Refinement TLS params.Method: refined / Origin x: 16.9886687926 Å / Origin y: 56.4334783352 Å / Origin z: 4.06471552646 Å
111213212223313233
T0.284035269491 Å2-0.0259847373699 Å20.00473141224426 Å2-0.336597749641 Å20.00187316835531 Å2--0.289396042273 Å2
L1.30742790368 °21.07487677905 °20.637990173755 °2-2.41904997759 °2-0.228715007551 °2--0.656237068851 °2
S-0.0478234626789 Å °0.0708078845132 Å °-0.0656247618412 Å °-0.108160434031 Å °0.0296762516175 Å °-0.0301684395001 Å °-0.032926559384 Å °0.162160663443 Å °0.0250697335428 Å °
Refinement TLS groupSelection details: all

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