9F4A | pdb_00009f4a

Interface between baseplate cup and extended tail tube/sheath of Klebsiella phage KP1 variant vB_Kpn_Lilla1

PDB DOI: https://doi.org/10.2210/pdb9F4A/pdb
EM Map EMD-50186: EMDB EMDataResource

Classification: VIRUS
Organism(s): Klebsiella phage KP1
Mutation(s): No

Deposited: 2024-04-26 Released: 2025-05-14
Deposition Author(s): Orlova, E.V., Isupov, M.N.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.95 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Baseplate cup of Klebsiella phage KP1 variant vB_Kpn_Lilla1

Orlova, E.V., Isupov, M.N.

To be published.

Macromolecule Content

Total Structure Weight: 11,021.56 kDa
Atom Count: 605,128
Modeled Residue Count: 77,559
Deposited Residue Count: 99,906
Unique protein chains: 14

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Long tail fiber proximal subunit	A [auth Le] B [auth Lf] C [auth Lg] D [auth Lh] E [auth Li] A [auth Le], B [auth Lf], C [auth Lg], D [auth Lh], E [auth Li], F [auth Lj], G [auth LS], H [auth LT], I [auth LU], J [auth LV], K [auth LW], L [auth LX], M [auth LY], N [auth LZ], O [auth La], P [auth Lb], Q [auth Lc], R [auth Ld]	1,281	Klebsiella phage KP1	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate tail tube cap	S [auth BM] T [auth BK] U [auth BO] V [auth BP] W [auth BL] S [auth BM], T [auth BK], U [auth BO], V [auth BP], W [auth BL], X [auth BN]	350	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2K9V618 (Klebsiella phage KP1) Explore A0A2K9V618 Go to UniProtKB: A0A2K9V618
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2K9V618
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate subunit	AA [auth BS] BA [auth BR] CA [auth BT] DA [auth BU] Y [auth BQ] AA [auth BS], BA [auth BR], CA [auth BT], DA [auth BU], Y [auth BQ], Z [auth BV]	308	Klebsiella phage KP1	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge protein gp6	EA [auth AX] FA [auth AW] GA [auth AT] HA [auth AS] IA [auth AV] EA [auth AX], FA [auth AW], GA [auth AT], HA [auth AS], IA [auth AV], JA [auth AU], KA [auth AR], LA [auth AQ], MA [auth AN], NA [auth AM], OA [auth AP], PA [auth AO]	655	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2K9V5R4 (Klebsiella phage KP1) Explore A0A2K9V5R4 Go to UniProtKB: A0A2K9V5R4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2K9V5R4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge protein gp7	QA [auth AY] RA [auth AZ] SA [auth A0] TA [auth A1] UA [auth A2] QA [auth AY], RA [auth AZ], SA [auth A0], TA [auth A1], UA [auth A2], VA [auth A3]	1,032	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2K9V5T9 (Klebsiella phage KP1) Explore A0A2K9V5T9 Go to UniProtKB: A0A2K9V5T9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2K9V5T9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge subunit	AB [auth A8] BB [auth A7] CB [auth Ad] DB [auth Ac] EB [auth Af] AB [auth A8], BB [auth A7], CB [auth Ad], DB [auth Ac], EB [auth Af], FB [auth Ae], GB [auth Ab], HB [auth Aa], WA [auth A4], XA [auth A9], YA [auth A6], ZA [auth A5]	341	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2Z4QAY9 (Klebsiella phage Mineola) Explore A0A2Z4QAY9 Go to UniProtKB: A0A2Z4QAY9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2Z4QAY9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge tail fiber connector	IB [auth LN] JB [auth LO] KB [auth LM] LB [auth LQ] MB [auth LR] IB [auth LN], JB [auth LO], KB [auth LM], LB [auth LQ], MB [auth LR], NB [auth LP], OB [auth LB], PB [auth LC], QB [auth LA], RB [auth LE], SB [auth LF], TB [auth LD], UB [auth LH], VB [auth LI], WB [auth LG], XB [auth LK], YB [auth LL], ZB [auth LJ]	303	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2K9V5S1 (Klebsiella phage KP1) Explore A0A2K9V5S1 Go to UniProtKB: A0A2K9V5S1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2K9V5S1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge protein gp10	AC [auth FA] BC [auth FB] CC [auth FC] DC [auth FJ] EC [auth FK] AC [auth FA], BC [auth FB], CC [auth FC], DC [auth FJ], EC [auth FK], FC [auth FL], GC [auth FS], HC [auth FT], IC [auth FU], JC [auth Fb], KC [auth Fc], LC [auth Fd], MC [auth Fk], NC [auth Fl], OC [auth Fm], PC [auth Ft], QC [auth Fu], RC [auth Fv]	607	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2K9V5S8 (Klebsiella phage KP1) Explore A0A2K9V5S8 Go to UniProtKB: A0A2K9V5S8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2K9V5S8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail sheath protein	AD [auth SL] AE [auth Si] BD [auth SH] BE [auth Sj] CD [auth SI] AD [auth SL], AE [auth Si], BD [auth SH], BE [auth Sj], CD [auth SI], CE [auth Sk], DD [auth SJ], DE [auth Sl], ED [auth SQ], EE [auth Sm], FD [auth SP], FE [auth Sn], GD [auth SM], GE [auth So], HD [auth SN], HE [auth Sp], ID [auth SO], JD [auth SR], KD [auth SW], LD [auth SS], MD [auth ST], ND [auth SU], OD [auth SV], PD [auth SX], QD [auth SY], RD [auth SZ], SC [auth SA], SD [auth Sa], TC [auth SB], TD [auth Sb], UC [auth SC], UD [auth Sc], VC [auth SD], VD [auth Sd], WC [auth SE], WD [auth Se], XC [auth SF], XD [auth Sf], YC [auth SK], YD [auth Sg], ZC [auth SG], ZD [auth Sh]	656	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2K9V5S7 (Klebsiella phage KP1) Explore A0A2K9V5S7 Go to UniProtKB: A0A2K9V5S7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2K9V5S7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail tube protein	AF [auth Te] BF [auth Tf] CF [auth Tg] DF [auth Th] EF [auth Ti] AF [auth Te], BF [auth Tf], CF [auth Tg], DF [auth Th], EF [auth Ti], FF [auth Tj], GF [auth Tk], HF [auth Tl], IE [auth TM], IF [auth Tm], JE [auth TN], JF [auth Tn], KE [auth TO], KF [auth To], LE [auth TP], LF [auth Tp], ME [auth TQ], MF [auth Tq], NE [auth TR], NF [auth Tr], OE [auth TW], OF [auth Ts], PE [auth TS], PF [auth Tt], QE [auth TT], QF [auth Tu], RE [auth TU], RF [auth Tv], SE [auth TV], TE [auth TX], UE [auth TY], VE [auth TZ], WE [auth Ta], XE [auth Tb], YE [auth Tc], ZE [auth Td]	163	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2K9V5T6 (Klebsiella phage KP1) Explore A0A2K9V5T6 Go to UniProtKB: A0A2K9V5T6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2K9V5T6
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
IraD/Gp25-like domain-containing protein	SF [auth AA] TF [auth AB] UF [auth AD] VF [auth AC] WF [auth AE] SF [auth AA], TF [auth AB], UF [auth AD], VF [auth AC], WF [auth AE], XF [auth AF]	136	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A0K1Y5J2 (Klebsiella phage JD18) Explore A0A0K1Y5J2 Go to UniProtKB: A0A0K1Y5J2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0K1Y5J2
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Reference Sequence

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| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative baseplate hub subunit	AG [auth BG], YF [auth BE], ZF [auth BF]	380	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A7T3TJP2 (Klebsiella phage vB_KpnM_BovinicusUrsus) Explore A0A7T3TJP2 Go to UniProtKB: A0A7T3TJP2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7T3TJP2
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Reference Sequence

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| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge subunit	BG [auth AL] CG [auth AI] DG [auth AG] EG [auth AK] FG [auth AH] BG [auth AL], CG [auth AI], DG [auth AG], EG [auth AK], FG [auth AH], GG [auth AJ]	212	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2K9V5R5 (Klebsiella phage KP1) Explore A0A2K9V5R5 Go to UniProtKB: A0A2K9V5R5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2K9V5R5
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Reference Sequence

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| 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate central spike protein	HG [auth BB], IG [auth BC], JG [auth BD]	576	Klebsiella phage KP1	Mutation(s): 0 EC: 3.2.1.17

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain KG [auth BB] MOL2 format, chain KG [auth BB] mmCIF format, chain KG [auth BB]	KG [auth BB]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain KG [auth BB] Interactions & Density Focus chain KG [auth BB]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.95 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	REFMAC	5.8.0258

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-14

Deposition Author(s):

Orlova, E.V.

Isupov, M.N.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-05-14
Type: Initial release

9F4A | pdb_00009f4a

Interface between baseplate cup and extended tail tube/sheath of Klebsiella phage KP1 variant vB_Kpn_Lilla1

Literature

Baseplate cup of Klebsiella phage KP1 variant vB_Kpn_Lilla1

Biological Assembly 1

Macromolecules

Entity ID: 1

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)