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Page 6 of 16 Varming et al. Microbiome Res Rep 2024;3:15 https://dx.doi.org/10.20517/mrr.2023.50

Table 1. Overview of crystal structures containing CI-NTD from TP901-1
PDB code Sequence* Comment Resolution Space group Cell Ref.
3ZHI MLKTDTSNRLK Q45AN48A- impaired 1.60 Å P 2 2 2 1 a = 29.62 Å [19]
1
1
QMAERNLKQV in DNA binding b = 43.59 Å
DILNLSIPFQKK c = 71.5 Å
FGIKLSKSTLSA α = 90˚
YVASVQSPDQN β = 90˚
RIYLLAKTLGV γ = 90˚
SEAWLMGRSH
HHHHH
3ZHM MLKTDTSNRLK Complex with DNA 2.60 Å P 2 2 2 1 a = 29.86 Å [19]
1
1
QIMAERNLKQV b = 64.07 Å
DILNLSIPFQKK c = 67.82 Å
FGIKLSKSTLSQ α = 90˚
YVNSVQSPDQN β = 90˚
RIYLLAKTLGVS γ = 90˚
EAWLMGRSHH
HHHH
5A7L MQTDTSNRLKQ Cleaved during long 2.10 Å P 2 2 2 a = 53.72 Å [20]
1
1
IMAERNLKQVD crystallization period b = 36.01 Å
ILNLSIPFQKKF - no DNA bound c = 38.77 Å
GIKLSKSTLSQY α = 90˚
VNSVQSPDQNR β = 90˚
IYLLAKTLGVSE γ = 90˚
AWLMGFDVPM
VESSKIENDSEN
IEETITVMKKLE
EPRQKVVLDTA
KIQLKEQDEQN
KVKQIEDYRLS
DRSHHHHHH
6TRI MQTDTSNRLKQ Complex with Mor 2.28 Å P 3 2 1 a = 94.41 Å [24]
IMAERNLKQVD b = 94.41 Å
ILNLSIPFQKKF c = 30.56 Å
GIKLSKSTLSQY α = 90˚
VNSVQSPDQNR β = 90˚
IYLLAKTLGV γ = 120˚
SEAWLMGFDVP
MVESSKIENDS
HHHHHH
8QAO MQTDTSNRLKQ 1.29 Å P 4 2 2 a = 48.4 Å This manuscript
1
3
IMAERNLKQVD b = 48.4 Å
ILNLSIPFQKKF c = 87.0 Å
GIKLSKSTLSQY α = 90˚
VNSVQSPDQNR β = 90˚
IYLLAKTLGV γ = 90˚
SEAWLMGFDVP
MVESSKIENDS
HHHHHH
*Non-native amino acids inserted or deviating from natural sequence are in bold. For 5A7L, the underlined amino acid is the last one visible in the
crystal structure. CI-NTD: N-terminal domain of Phage repressor.

Modeling with AlphaFold2
AlphaFold2 (AF2) models for individual φ13 proteins were either from the Alphafold database (Q2FWP6
[36]
[35]
and Q2FWP7, model version 4) or constructed using the Colab version of Alphafold2 using default
parameters. TP901-1 CI-NTD was modeled using the full-length TP901-1 CI wild-type sequence with no
templates. For the φ13 CI-NTD (residues 1-88)/Mor complex, the experimental complex of TP901-1
CI-NTD and Mor (PDB code 6TRI, Figure 1D) was used as template, and in parallel models were generated
also without template and with automatic template recognition.