9H4P | pdb_00009h4p

Tail of full Haloferax tailed virus 1

PDB DOI: https://doi.org/10.2210/pdb9H4P/pdb
EM Map EMD-51866: EMDB EMDataResource

Classification: VIRUS
Organism(s): Haloferax tailed virus 1
Mutation(s): No

Deposited: 2024-10-21 Released: 2025-08-27
Deposition Author(s): Zhang, D., Daum, B., Isupov, M.N., McLaren, M.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.44 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

CryoEM structure of Haloferax tailed virus

Zhang, D., Daum, B., Isupov, M.N., McLaren, M., Oksanen, H., Quax, T.E.F., Schwarzer, S., Gold, V.A.M., Stuart, W.

To be published.

Macromolecule Content

Total Structure Weight: 2,949.19 kDa
Atom Count: 179,352
Modeled Residue Count: 23,358
Deposited Residue Count: 26,925
Unique protein chains: 7

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate hub	A [auth BD], B [auth BE], C [auth BF]	954	Haloferax tailed virus 1	Mutation(s): 0
UniProt
Find proteins for A0A410N6T6 (Haloferax tailed virus 1) Explore A0A410N6T6 Go to UniProtKB: A0A410N6T6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A410N6T6
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phate tail tape measure protein	D [auth QG] E [auth QH] F [auth QI] G [auth QJ] H [auth QE] D [auth QG], E [auth QH], F [auth QI], G [auth QJ], H [auth QE], I [auth QF]	341	Haloferax tailed virus 1	Mutation(s): 0
UniProt
Find proteins for A0A410N6W4 (Haloferax tailed virus 1) Explore A0A410N6W4 Go to UniProtKB: A0A410N6W4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A410N6W4
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate to tube adapter protein gp41	J [auth BA], K [auth BB], L [auth BC]	285	Haloferax tailed virus 1	Mutation(s): 0
UniProt
Find proteins for A0A410N6X8 (Haloferax tailed virus 1) Explore A0A410N6X8 Go to UniProtKB: A0A410N6X8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A410N6X8
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail tube protein	AA [auth SO] AB [auth Sc] BA [auth SP] BB [auth Sd] CA [auth SQ] AA [auth SO], AB [auth Sc], BA [auth SP], BB [auth Sd], CA [auth SQ], CB [auth B1], DA [auth SR], DB [auth B2], EA [auth SB], EB [auth B3], FA [auth SA], FB [auth B4], GA [auth SC], GB [auth B5], HA [auth SD], HB [auth B6], IA [auth SE], IB [auth Sw], JA [auth SF], JB [auth Sx], KA [auth Sk], KB [auth Sy], LA [auth Sl], LB [auth Sz], M [auth SG], MA [auth Sm], MB [auth S1], N [auth SH], NA [auth Sn], NB [auth S2], O [auth SI], OA [auth So], OB [auth Sq], P [auth SJ], PA [auth Sp], PB [auth Sr], Q [auth SK], QA [auth Se], QB [auth Ss], R [auth SL], RA [auth Sf], RB [auth St], S [auth SS], SA [auth Sg], SB [auth Su], T [auth ST], TA [auth Sh], TB [auth Sv], U [auth SU], UA [auth Si], UB [auth P1], V [auth SV], VA [auth Sj], VB [auth P2], W [auth SW], WA [auth SY], WB [auth P3], X [auth SX], XA [auth SZ], XB [auth P4], Y [auth SM], YA [auth Sa], YB [auth P5], Z [auth SN], ZA [auth Sb], ZB [auth P6]	158	Haloferax tailed virus 1	Mutation(s): 0
UniProt
Find proteins for A0A410N6U0 (Haloferax tailed virus 1) Explore A0A410N6U0 Go to UniProtKB: A0A410N6U0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A410N6U0
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
SPP1 gp17-like tail completion protein	AC [auth Pa] BC [auth Pb] CC [auth Pc] DC [auth Pd] EC [auth Pe] AC [auth Pa], BC [auth Pb], CC [auth Pc], DC [auth Pd], EC [auth Pe], FC [auth Pf]	157	Haloferax tailed virus 1	Mutation(s): 0
UniProt
Find proteins for A0A410N6U9 (Haloferax tailed virus 1) Explore A0A410N6U9 Go to UniProtKB: A0A410N6U9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A410N6U9
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
HK97 gp6-like/SPP1 gp15-like head-tail connector	GC [auth PT] HC [auth PM] IC [auth PN] JC [auth PO] KC [auth PP] GC [auth PT], HC [auth PM], IC [auth PN], JC [auth PO], KC [auth PP], LC [auth PQ], MC [auth PR], NC [auth PS], OC [auth PU], PC [auth PV], QC [auth PW], RC [auth PX]	141	Haloferax tailed virus 1	Mutation(s): 0
UniProt
Find proteins for A0A410N6S3 (Haloferax tailed virus 1) Explore A0A410N6S3 Go to UniProtKB: A0A410N6S3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A410N6S3
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Portal protein	AD [auth PI] BD [auth PJ] CD [auth PK] DD [auth PL] SC [auth PA] AD [auth PI], BD [auth PJ], CD [auth PK], DD [auth PL], SC [auth PA], TC [auth PB], UC [auth PC], VC [auth PD], WC [auth PE], XC [auth PF], YC [auth PG], ZC [auth PH]	675	Haloferax tailed virus 1	Mutation(s): 0
UniProt
Find proteins for A0A410N6Q2 (Haloferax tailed virus 1) Explore A0A410N6Q2 Go to UniProtKB: A0A410N6Q2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A410N6Q2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain ED [auth BD] SDF format, chain FD [auth BE] SDF format, chain GD [auth BF] SDF format, chain HD [auth PT] SDF format, chain ID [auth PM] SDF format, chain JD [auth PN] SDF format, chain KD [auth PO] SDF format, chain LD [auth PP] SDF format, chain MD [auth PQ] SDF format, chain ND [auth PR] SDF format, chain OD [auth PS] SDF format, chain PD [auth PU] SDF format, chain QD [auth PU] SDF format, chain RD [auth PV] SDF format, chain SD [auth PW] MOL2 format, chain ED [auth BD] MOL2 format, chain FD [auth BE] MOL2 format, chain GD [auth BF] MOL2 format, chain HD [auth PT] MOL2 format, chain ID [auth PM] MOL2 format, chain JD [auth PN] MOL2 format, chain KD [auth PO] MOL2 format, chain LD [auth PP] MOL2 format, chain MD [auth PQ] MOL2 format, chain ND [auth PR] MOL2 format, chain OD [auth PS] MOL2 format, chain PD [auth PU] MOL2 format, chain QD [auth PU] MOL2 format, chain RD [auth PV] MOL2 format, chain SD [auth PW] mmCIF format, chain ED [auth BD] mmCIF format, chain FD [auth BE] mmCIF format, chain GD [auth BF] mmCIF format, chain HD [auth PT] mmCIF format, chain ID [auth PM] mmCIF format, chain JD [auth PN] mmCIF format, chain KD [auth PO] mmCIF format, chain LD [auth PP] mmCIF format, chain MD [auth PQ] mmCIF format, chain ND [auth PR] mmCIF format, chain OD [auth PS] mmCIF format, chain PD [auth PU] mmCIF format, chain QD [auth PU] mmCIF format, chain RD [auth PV] mmCIF format, chain SD [auth PW]	ED [auth BD] FD [auth BE] GD [auth BF] HD [auth PT] ID [auth PM] ED [auth BD], FD [auth BE], GD [auth BF], HD [auth PT], ID [auth PM], JD [auth PN], KD [auth PO], LD [auth PP], MD [auth PQ], ND [auth PR], OD [auth PS], PD [auth PU], QD [auth PU], RD [auth PV], SD [auth PW]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain ED [auth BD] Focus chain FD [auth BE] Focus chain GD [auth BF] Focus chain HD [auth PT] Focus chain ID [auth PM] Focus chain JD [auth PN] Focus chain KD [auth PO] Focus chain LD [auth PP] Focus chain MD [auth PQ] Focus chain ND [auth PR] Focus chain OD [auth PS] Focus chain PD [auth PU] Focus chain QD [auth PU] Focus chain RD [auth PV] Focus chain SD [auth PW] Interactions & Density Focus chain ED [auth BD] Focus chain FD [auth BE] Focus chain GD [auth BF] Focus chain HD [auth PT] Focus chain ID [auth PM] Focus chain JD [auth PN] Focus chain KD [auth PO] Focus chain LD [auth PP] Focus chain MD [auth PQ] Focus chain ND [auth PR] Focus chain OD [auth PS] Focus chain PD [auth PU] Focus chain QD [auth PU] Focus chain RD [auth PV] Focus chain SD [auth PW]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIP Query on HIP	AD [auth PI] BD [auth PJ] CD [auth PK] DD [auth PL] SC [auth PA] AD [auth PI], BD [auth PJ], CD [auth PK], DD [auth PL], SC [auth PA], TC [auth PB], UC [auth PC], VC [auth PD], WC [auth PE], XC [auth PF], YC [auth PG], ZC [auth PH]	L-PEPTIDE LINKING	C₆ H₁₁ N₃ O₅ P		HIS