9K3M: Microviridae PJNS001

The structure of Microviridae PJNS001. Determined by electron microscopy at 2.68 Å resolution. Released 13 Aug 2025.

Method
Electron microscopy
Resolution
2.68 Å
Organism
Microviridae
Chains
180
Atoms
302,160
Mol. weight
4311.13 kDa
Released
13 Aug 2025

Explore 9K3M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9K3M contains 1,560 α-helices and 2,880 β-strands across 180 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A, AB, AE, BC, BF, CA, CD, D, DB, DE, EC, EF, F, FA, FD, GB, GE, HC, HF, I, IA, ID, JB, JE, KC, KF, LA, LD, M, MB, ME, NC, NF, OA, OD, P, PB, PE, QC, QF, RA, RD, S, SB, SE, TC, TF, UA, UD, VB, VE, W, WC, WF, XA, XD, YB, YE, Z and ZC: 23 helices, 30 β-strands

ElementResiduesLengthSheet
β-strand10-134121
β-strand17-237121
β-strand27-282122
β-strand29-368123
β-strand41-5212121
α-helix53-542
β-strand551124
β-strand611125
β-strand63-7311123
α-helix75-784
α-helix81-888
α-helix92-965
β-strand97-993126
α-helix113-1153
β-strand119-1213126
α-helix122-13514
α-helix142-1432
α-helix149-1513
α-helix1531
β-strand161-1622122
β-strand1641127
α-helix165-1673
β-strand183-1853128
β-strand190-1923129
α-helix193-21119
α-helix216-2227
α-helix229-2324
β-strand236-24510123
β-strand247-2515130
β-strand261-2655130
β-strand266-27712121
β-strand282-29110123
β-strand2961131
β-strand2991132
α-helix302-3054
α-helix311-3144
α-helix318-3214
α-helix325-3262
β-strand327-3304133
α-helix331-3333
β-strand3351132
β-strand343-3464133
α-helix350-3523
β-strand358-359253
α-helix361-3633
β-strand3721131
α-helix380-3845
β-strand3851127
α-helix388-3947
β-strand3951124
β-strand3971134
β-strand403-41614121
α-helix420-4245
Chains AA, AD, B, BB, BE, CC, CF, DA, DD, E, EB, EE, FC, FF, G, GA, GD, HB, HE, IC, IF, JA, JD, K, KB, KE, LC, LF, MA, MD, N, NB, NE, OC, OF, PA, PD, Q, QB, QE, RC, RF, SA, SD, T, TB, TE, UC, UF, VA, VD, WB, WE, X, XC, XF, YA, YD, ZB and ZE: 2 helices, 15 β-strands
ElementResiduesLengthSheet
β-strand2-32930
β-strand6-72931
β-strand15-173932
β-strand22-232932
β-strand261933
α-helix29-302
β-strand311933
β-strand39-4911932
β-strand52-6110933
α-helix62-632
β-strand70-8112932
β-strand87-9610933
β-strand108-1103933
β-strand120-13011932
β-strand139-15012933
β-strand153-16311932
β-strand1711908
Chains AC, AF, BA, BD, C, CB, CE, DC, DF, EA, ED, FB, FE, GC, GF, H, HA, HD, IB, IE, J, JC, JF, KA, KD, L, LB, LE, MC, MF, NA, ND, O, OB, OE, PC, PF, QA, QD, R, RB, RE, SC, SF, TA, TD, UB, UE, V, VC, VF, WA, WD, XB, XE, Y, YC, YF, ZA and ZD: 1 helix, 3 β-strands
ElementResiduesLengthSheet
β-strand7-82855
β-strand10-112853
α-helix16-172
β-strand181874

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Capsid protein FA, AB, AE, BC, BF, CA, CD, D, DB, DE, EC, EF, F, FA, FD, GB, GE, HC, HF, I, IA, ID, JB, JE, KC, KF, LA, LD, M, MB, ME, NC, NF, OA, OD, P, PB, PE, QC, QF, RA, RD, S, SB, SE, TC, TF, UA, UD, VB, VE, W, WC, WF, XA, XD, YB, YE, Z, ZCprotein427MicroviridaeQ2LLZ1
Major spike protein GAA, AD, B, BB, BE, CC, CF, DA, DD, E, EB, EE, FC, FF, G, GA, GD, HB, HE, IC, IF, JA, JD, K, KB, KE, LC, LF, MA, MD, N, NB, NE, OC, OF, PA, PD, Q, QB, QE, RC, RF, SA, SD, T, TB, TE, UC, UF, VA, VD, WB, WE, X, XC, XF, YA, YD, ZB, ZEprotein175MicroviridaeA0A5J6T840
DNA-binding protein JAC, AF, BA, BD, C, CB, CE, DC, DF, EA, ED, FB, FE, GC, GF, H, HA, HD, IB, IE, J, JC, JF, KA, KD, L, LB, LE, MC, MF, NA, ND, O, OB, OE, PC, PF, QA, QD, R, RB, RE, SC, SF, TA, TD, UB, UE, V, VC, VF, WA, WD, XB, XE, Y, YC, YF, ZA, ZDprotein38MicroviridaeP69592
Sequence of entity 1 (A, AB, AE, BC, BF, CA, CD, D, DB, DE, EC, EF, F, FA, FD, GB, GE, HC, HF, I, IA, ID, JB, JE, KC, KF, LA, LD, M, MB, ME, NC, NF, OA, OD, P, PB, PE, QC, QF, RA, RD, S, SB, SE, TC, TF, UA, UD, VB, VE, W, WC, WF, XA, XD, YB, YE, Z, ZC), FASTA
>9K3M_1 Capsid protein F (chains A, AB, AE, BC, BF, CA, CD, D, DB, DE, EC, EF, F, FA, FD, GB, GE, HC, HF, I, IA, ID, JB, JE, KC, KF, LA, LD, M, MB, ME, NC, NF, OA, OD, P, PB, PE, QC, QF, RA, RD, S, SB, SE, TC, TF, UA, UD, VB, VE, W, WC, WF, XA, XD, YB, YE, Z, ZC)
MSNVQTGAERMPHDLSHLGFLAGQIGRLITISTTPVIAGDSFEMDAVGALRLSPLRRGLA
IDSTVDIFTFYVPHRHVYGEQWIKFMKDGVNAAPLPTVNTTGYIDHAAFLGTINPDTNKI
PKHLFQGYLNIYNNYFKAPWMPDRTEANPNQLNEDDARYGFRCCHLKNIWTAPLPPETEL
SRQMTTSTTSIDIMGLQAAYANLHTDQERDYFMQRYRDVISSFGGKTSYDADNRPLLVMR
SNFWASGYDVDGTDQTSLGQFSGRVQQTYKHSVPRFFVPEHGTMFTLALVRFPPTATKEI
QYLNAKGALTYTDIAGDPALYGNLPPREISMKDVFRSGDASKKFKIAEGQWYRYAPSYVS
PAYHLLEGFPFIQEPPSGDLQERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRNLPTT
RDSIMTS
Sequence of entity 2 (AA, AD, B, BB, BE, CC, CF, DA, DD, E, EB, EE, FC, FF, G, GA, GD, HB, HE, IC, IF, JA, JD, K, KB, KE, LC, LF, MA, MD, N, NB, NE, OC, OF, PA, PD, Q, QB, QE, RC, RF, SA, SD, T, TB, TE, UC, UF, VA, VD, WB, WE, X, XC, XF, YA, YD, ZB, ZE), FASTA
>9K3M_2 Major spike protein G (chains AA, AD, B, BB, BE, CC, CF, DA, DD, E, EB, EE, FC, FF, G, GA, GD, HB, HE, IC, IF, JA, JD, K, KB, KE, LC, LF, MA, MD, N, NB, NE, OC, OF, PA, PD, Q, QB, QE, RC, RF, SA, SD, T, TB, TE, UC, UF, VA, VD, WB, WE, X, XC, XF, YA, YD, ZB, ZE)
MFQTFISRHNSNFFSDKLVATSVTPASLAPVLQTPKAASSTLYFNQLTVNAGNGGFLHCI
QMDTSVNAANQVVSVGADIAFDADPKFFACLVRFESASVPTTLPTDYDVYPLDGRHDGGY
YTVKDCVTIDVLPREPGNNVYVGFMVWSNFTATKCRGLVSLNQVIKEIICLQPLK
Sequence of entity 3 (AC, AF, BA, BD, C, CB, CE, DC, DF, EA, ED, FB, FE, GC, GF, H, HA, HD, IB, IE, J, JC, JF, KA, KD, L, LB, LE, MC, MF, NA, ND, O, OB, OE, PC, PF, QA, QD, R, RB, RE, SC, SF, TA, TD, UB, UE, V, VC, VF, WA, WD, XB, XE, Y, YC, YF, ZA, ZD), FASTA
>9K3M_3 DNA-binding protein J (chains AC, AF, BA, BD, C, CB, CE, DC, DF, EA, ED, FB, FE, GC, GF, H, HA, HD, IB, IE, J, JC, JF, KA, KD, L, LB, LE, MC, MF, NA, ND, O, OB, OE, PC, PF, QA, QD, R, RB, RE, SC, SF, TA, TD, UB, UE, V, VC, VF, WA, WD, XB, XE, Y, YC, YF, ZA, ZD)
MSKGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF

Primary citation

Structural basis for Salmonella infection by two Microviridae phages. Hu, W., Liu, Z., Wei, Y. et al. Commun Biol (2025) 8:1166-1166. DOI 10.1038/s42003-025-08595-7 · PubMed

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