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- PDB-9dcy: Crystal Structure of Designed allosteric facilitated dissociation... -

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Basic information

Entry
Database: PDB / ID: 9dcy
TitleCrystal Structure of Designed allosteric facilitated dissociation switch AS1 in complex state HE
Components
  • Designed allosteric facilitated dissociation switch AS1 E
  • Designed allosteric facilitated dissociation switch AS1 H
KeywordsDE NOVO PROTEIN / design model / Effector / kinetics and dynamics / Protein-protein interactions
Function / homologyS-1,2-PROPANEDIOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBera, A.K. / Broerman, A. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2025
Title: Design of facilitated dissociation enables timing of cytokine signalling.
Authors: Broerman, A.J. / Pollmann, C. / Zhao, Y. / Lichtenstein, M.A. / Jackson, M.D. / Tessmer, M.H. / Ryu, W.H. / Ogishi, M. / Abedi, M.H. / Sahtoe, D.D. / Allen, A. / Kang, A. / De La Cruz, J. / ...Authors: Broerman, A.J. / Pollmann, C. / Zhao, Y. / Lichtenstein, M.A. / Jackson, M.D. / Tessmer, M.H. / Ryu, W.H. / Ogishi, M. / Abedi, M.H. / Sahtoe, D.D. / Allen, A. / Kang, A. / De La Cruz, J. / Brackenbrough, E. / Sankaran, B. / Bera, A.K. / Zuckerman, D.M. / Stoll, S. / Garcia, K.C. / Praetorius, F. / Piehler, J. / Baker, D.
History
DepositionAug 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 8, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Designed allosteric facilitated dissociation switch AS1 H
B: Designed allosteric facilitated dissociation switch AS1 E
C: Designed allosteric facilitated dissociation switch AS1 H
D: Designed allosteric facilitated dissociation switch AS1 E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2026
Polymers63,0504
Non-polymers1522
Water1,06359
1
A: Designed allosteric facilitated dissociation switch AS1 H
B: Designed allosteric facilitated dissociation switch AS1 E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6013
Polymers31,5252
Non-polymers761
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-19 kcal/mol
Surface area13370 Å2
MethodPISA
2
C: Designed allosteric facilitated dissociation switch AS1 H
D: Designed allosteric facilitated dissociation switch AS1 E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6013
Polymers31,5252
Non-polymers761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-19 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.448, 35.983, 88.903
Angle α, β, γ (deg.)90.000, 109.626, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Designed allosteric facilitated dissociation switch AS1 H


Mass: 28433.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide Designed allosteric facilitated dissociation switch AS1 E


Mass: 3091.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M 1,6-Hexanediol, 0.2M 1-Butanol, 0.2M 1,2-Propanediol, 0.2M 2-Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol, Sodium HEPES; MOPS (acid) pH 7.5 and 40% v/v PEG 500* MME; 20 % w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.35→47.98 Å / Num. obs: 19956 / % possible obs: 99.66 % / Redundancy: 4.8 % / Biso Wilson estimate: 31.36 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.044 / Net I/σ(I): 8.7
Reflection shellResolution: 2.35→2.47 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 1.88 / Num. unique obs: 2831 / CC1/2: 0.692 / Rpim(I) all: 0.19 / % possible all: 99.89

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Processing

Software
NameVersionClassification
PHENIXdev_4761refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→47.98 Å / SU ML: 0.2923 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 24.8525
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2435 1025 5.14 %
Rwork0.1936 18931 -
obs0.1961 19956 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.83 Å2
Refinement stepCycle: LAST / Resolution: 2.35→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4340 0 10 59 4409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00144364
X-RAY DIFFRACTIONf_angle_d0.32575840
X-RAY DIFFRACTIONf_chiral_restr0.0346722
X-RAY DIFFRACTIONf_plane_restr0.0023738
X-RAY DIFFRACTIONf_dihedral_angle_d12.23851730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.470.31841550.22262676X-RAY DIFFRACTION99.89
2.47-2.630.30041400.23532679X-RAY DIFFRACTION99.86
2.63-2.830.29891440.23432652X-RAY DIFFRACTION99.61
2.83-3.120.29051490.21542690X-RAY DIFFRACTION99.58
3.12-3.570.27091420.20222724X-RAY DIFFRACTION99.51
3.57-4.490.20161520.16462701X-RAY DIFFRACTION99.93
4.5-47.980.19071430.17122809X-RAY DIFFRACTION99.26

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