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

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Basic information

Entry
Database: PDB / ID: 8gji
TitleDe novo design of high-affinity protein binders to bioactive helical peptides
Components
  • GCG binder
  • Glucagon
KeywordsDE NOVO PROTEIN / Alpha-helical peptides / protein design / diffusion / deep learning
Function / homology
Function and homology information


glucagon receptor binding / : / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of insulin secretion / response to activity / hormone activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / glucose homeostasis / negative regulation of apoptotic process / extracellular space
Similarity search - Function
Glucagon / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones
Similarity search - Domain/homology
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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
DepositionMar 15, 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

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Assembly

Deposited unit
A: GCG binder
B: Glucagon


Theoretical massNumber of molelcules
Total (without water)24,0632
Polymers24,0632
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-17 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.269, 50.920, 91.927
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein GCG binder


Mass: 20576.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide Glucagon


Mass: 3486.781 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P01273
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 1.6 Å3/Da / Density % sol: 19.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Ammonium chloride 0.1 M Tris pH 8 20% (w/v) PEG 6000

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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 S 16M / Detector: PIXEL / Date: Mar 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.81→91.93 Å / Num. obs: 13875 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 35.08 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.053 / Net I/σ(I): 8.3
Reflection shellResolution: 1.81→1.88 Å / Redundancy: 6 % / Rmerge(I) obs: 1.581 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1327 / CC1/2: 0.459 / Rpim(I) all: 0.761 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIXdev_4761refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→45.96 Å / SU ML: 0.2881 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.4549
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2552 1378 9.99 %
Rwork0.208 12410 -
obs0.213 13788 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.18 Å2
Refinement stepCycle: LAST / Resolution: 1.81→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1579 0 0 24 1603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01181592
X-RAY DIFFRACTIONf_angle_d1.11612111
X-RAY DIFFRACTIONf_chiral_restr0.0587234
X-RAY DIFFRACTIONf_plane_restr0.0073264
X-RAY DIFFRACTIONf_dihedral_angle_d17.6135661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.880.44851320.37521196X-RAY DIFFRACTION97.43
1.88-1.950.40221360.34231225X-RAY DIFFRACTION99.42
1.95-2.040.3281350.26281208X-RAY DIFFRACTION99.48
2.04-2.150.31331350.21821224X-RAY DIFFRACTION99.49
2.15-2.290.23581370.19331225X-RAY DIFFRACTION99.49
2.29-2.460.24951350.18811221X-RAY DIFFRACTION99.27
2.46-2.710.25461400.18341256X-RAY DIFFRACTION99.43
2.71-3.10.24131380.20091249X-RAY DIFFRACTION99.5
3.1-3.910.26461420.1991277X-RAY DIFFRACTION99.37
3.91-45.960.22661480.20221329X-RAY DIFFRACTION98.27
Refinement TLS params.Method: refined / Origin x: 1.47497523339 Å / Origin y: 3.36439985481 Å / Origin z: 11.5039442839 Å
111213212223313233
T0.250813746354 Å20.0222993493261 Å20.00192126908365 Å2-0.259234219097 Å20.0146805302058 Å2--0.251595272008 Å2
L1.14625192976 °20.921270072047 °20.248970292944 °2-1.53127061149 °2-0.204521804356 °2--1.18994275804 °2
S-0.0131934217752 Å °-0.0683336280336 Å °0.0209040243216 Å °-0.139903516681 Å °-0.0651272780829 Å °0.019271111616 Å °-0.0611262807672 Å °-0.0059412971111 Å °-0.00267741834013 Å °
Refinement TLS groupSelection details: all

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