7SOZ

Replication Initiator Protein REPE54 and cognate DNA sequence with terminal three prime phosphates chemically crosslinked (5 mg/mL EDC, 12 hours).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Modular Protein-DNA Cocrystals as Precise, Programmable Assembly Scaffolds.

Orun, A.R.Shields, E.T.Dmytriw, S.Vajapayajula, A.Slaughter, C.K.Snow, C.D.

(2023) ACS Nano 17: 13110-13120

  • DOI: https://doi.org/10.1021/acsnano.2c07282
  • Primary Citation of Related Structures:  
    7SDP, 7SOZ, 7U6K, 7U7O, 7UFX, 7UOG, 7UR0, 7UV6, 7UV7, 7UXY, 8D86

  • PubMed Abstract: 

    High-precision nanomaterials to entrap DNA-binding molecules are sought after for applications such as controlled drug delivery and scaffold-assisted structural biology. Here, we engineered protein-DNA cocrystals to serve as scaffolds for DNA-binding molecules. The designed cocrystals, isoreticular cocrystals, contain DNA-binding protein and cognate DNA blocks where the DNA-DNA junctions stack end-to-end. Furthermore, the crystal symmetry allows topology preserving (isoreticular) expansion of the DNA stack without breaking protein-protein contacts, hence providing larger solvent channels for guest diffusion. Experimentally, the resulting designed isoreticular cocrystal adopted an interpenetrating I 222 lattice, a phenomenon previously observed in metal-organic frameworks (MOFs). The interpenetrating lattice crystallized dependably in the same space group despite myriad modifications at the DNA-DNA junctions. Assembly was modular with respect to the DNA inserted for expansion, providing an interchangeable DNA sequence for guest-specified scaffolding. Also, the DNA-DNA junctions were tunable, accommodating varied sticky base overhang lengths and terminal phosphorylation. As a proof of concept, we used the interpenetrating scaffold crystals to separately entrap three distinct guest molecules during crystallization. Isoreticular cocrystal design offers a route to a programmable scaffold for DNA-binding molecules, and the design principles may be applied to existing cocrystals to develop scaffolding materials.


  • Organizational Affiliation

    Department of Chemistry, Colorado State University, 1301 Center Ave., Fort Collins, Colorado 80523, United States.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RepB family plasmid replication initiator protein263Escherichia coliMutation(s): 1 
Gene Names: 
repERepErepE_1repE_2A9P13_27925ACN81_13795AKG29_00005AM270_25025AM446_00510AM465_27515APX88_12585B9N33_25510BANRA_05159BANRA_05459BANRA_05682BANRA_05685BE930_02070BE963_00170BFD68_26000BIU72_26315BK334_12915BON69_00085BON86_02490BTQ06_15345BvCmsKSNP073_00547BvCmsKSNP081_03109C5F73_28740C6669_28055CCZ17_26065CDL37_25390CUB99_27055D0X26_27580D2188_23935D6C57_20535D6T60_26250D9G11_25395D9J60_24770DL545_01395DLU82_26460DM102_26130DMZ50_25125DN808_25760DNQ45_17165DP277_27365E0L04_25075E4K51_24545E5P24_21725E5S56_18100EA191_27055EA214_24280EA233_23655EA834_24495EC3234A_223c00190ECTO124_05352EGT48_00285EIZ93_24320EJC75_00275ELT22_23490ELT31_24090ELT31_26285ELT33_22145ELU82_24155ELU85_22525ELV00_24275ELV13_22345ELV22_21715ELV22_26415ELV24_23180ELV24_26400ELX56_23450ELX56_26570ELX68_22815ELX68_25985ELX70_23725ELX70_27680ELX79_25360ELX79_27900ELX83_21670ELX83_26905ELY23_22635ELY23_25820ELY24_18745ELY24_28685ELY48_20420ELY48_27905ELY50_22820ELY50_26360EPS70_23590EQ823_22980EQ830_17775ERS085362_04815ERS150873_04643EVY14_01415ExPECSC065_01123F0L67_01685F7O57_26240FAF34_003215FKO60_21690FVA71_27640G3565_27065G4276_24945G4280_26215G5603_23890G5632_20220G5697_22865G5V60_25015GE057_22565GE087_25865GE096_23180GE400_25540GE558_24730GKE29_21080GKE58_20235GKE60_20510GKE79_19945GKE87_19350GQY14_24020GRC73_23425HGR17_18615HGR87_25030HGR88_23710HGS97_17250HH117_25695HH456_004544HH814_004957HIO03_005020HIZ44_004944HJ359_004520HJI79_004024HJL93_004672HJM89_004053HJT66_004466HKA14_004545HL186_24195HLI97_004832HMT01_25475HMT08_23785HNV94_24925HNX16_24825HNX34_21985HPE39_26560HR075_24855HV055_25390HV303_25935HVW09_26465HVW60_23575HVW98_24555HVX24_22925HVX51_24935HVY93_24645HVZ71_26895IB283_25495IPF_37pCTXM15_EC8_00107RCS105_pI0165RCS57_p0140RCS59_P0063SAMEA4370330_00165SAMEA4370365_00054SY51_26335WP4S17E03_P11650WP4S18E08_P10410YDC107_5106

UniProt
Find proteins for P03856 (Escherichia coli (strain K12))
Explore P03856 
Go to UniProtKB:  P03856
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03856
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*A)-3')22Escherichia coli
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*A)-3')22Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.993α = 90
b = 79.181β = 123.023
c = 74.903γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States2003748

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-11-01
    Changes: Database references