29KH | pdb_000029kh

Outer capsid of the ranavirus Frog Virus 3

PDB DOI: https://doi.org/10.2210/pdb29KH/pdb
EM Map EMD-57237: EMDB EMDataResource

Classification: VIRUS
Organism(s): Frog virus 3
Mutation(s): No

Deposited: 2026-03-17 Released: 2026-10-21
Deposition Author(s): Sandoval-Valencia, J.D., Shah, P.N.M., Stuart, D., Fry, E.
Funding Organization(s): Wellcome Trust, Medical Research Council (MRC, United Kingdom), CAMS Innovation Fund for Medical Sciences (CIFMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Lessons for constructing and deconstructing giant viruses from the structure of Frog Virus 3

Sandoval-Valencia, J.D., Shah, P.N.M., Stuart, D., Fry, E.

To be published.

Macromolecule Content

Total Structure Weight: 5,405.49 kDa
Atom Count: 330,022
Modeled Residue Count: 43,436
Deposited Residue Count: 50,117
Unique protein chains: 10

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vp34	A [auth A1] AA [auth F2] AB [auth K3] AC [auth P1] AD [auth U1] A [auth A1], AA [auth F2], AB [auth K3], AC [auth P1], AD [auth U1], B [auth A2], BC [auth P2], BD [auth U2], CD [auth U3], CE [auth b1], DE [auth b2], EA [auth G1], EB [auth L1], F [auth B1], FA [auth G2], FB [auth L2], FC [auth Q1], G [auth B2], GB [auth L3], GC [auth Q2], GD [auth V1], HD [auth V2], HE [auth c2], ID [auth V3], IE [auth c3], JA [auth H1], K [auth C1], KB [auth M1], KC [auth R1], L [auth C2], LB [auth M2], LC [auth R2], MB [auth M3], ME [auth d1], NA [auth I1], NE [auth d2], OA [auth I2], P [auth D1], PC [auth S1], Q [auth D2], QB [auth N1], QC [auth S2], RB [auth N2], RE [auth e1], SA [auth J1], TA [auth J2], U [auth E1], UA [auth J3], UC [auth T1], V [auth E2], VB [auth O1], VC [auth T2], VE [auth f1], WB [auth O2], WC [auth T3], WE [auth f3], YA [auth K1], YD [auth a3], Z [auth F1], ZA [auth K2]	106	Frog virus 3	Mutation(s): 0
UniProt
Find proteins for Q6GZU2 (Frog virus 3 (isolate Goorha)) Explore Q6GZU2 Go to UniProtKB: Q6GZU2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6GZU2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	AE [auth ab] BA [auth Fa] BB [auth Ka] BE [auth ac] C [auth Aa] AE [auth ab], BA [auth Fa], BB [auth Ka], BE [auth ac], C [auth Aa], CA [auth Fb], CB [auth Kb], CC [auth Pa], D [auth Ab], DA [auth Fc], DB [auth Kc], DC [auth Pb], DD [auth Ua], E [auth Ac], EC [auth Pc], ED [auth Ub], EE [auth ba], FD [auth Uc], FE [auth bb], GA [auth Ga], GE [auth bc], H [auth Ba], HA [auth Gb], HB [auth La], HC [auth Qa], I [auth Bb], IA [auth Gc], IB [auth Lb], IC [auth Qb], J [auth Bc], JB [auth Lc], JC [auth Qc], JD [auth Va], JE [auth ca], KA [auth Ha], KD [auth Vb], KE [auth cb], LA [auth Hb], LD [auth Vc], LE [auth cc], M [auth Ca], MA [auth Hc], MC [auth Ra], N [auth Cb], NB [auth Ma], NC [auth Rb], O [auth Cc], OB [auth Mb], OC [auth Rc], OE [auth da], PA [auth Ia], PB [auth Mc], PE [auth db], QA [auth Ib], QE [auth dc], R [auth Da], RA [auth Ic], RC [auth Sa], S [auth Db], SB [auth Na], SC [auth Sb], SE [auth ea], T [auth Dc], TB [auth Nb], TC [auth Sc], TE [auth eb], UB [auth Nc], UE [auth ec], VA [auth Ja], W [auth Ea], WA [auth Jb], X [auth Eb], XA [auth Jc], XB [auth Oa], XC [auth Ta], XE [auth fa], Y [auth Ec], YB [auth Ob], YC [auth Tb], YE [auth fb], ZB [auth Oc], ZC [auth Tc], ZD [auth aa], ZE [auth fc]	463	Frog virus 3	Mutation(s): 0
UniProt
Find proteins for C5HJX8 (Frog virus 3) Explore C5HJX8 Go to UniProtKB: C5HJX8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C5HJX8
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Vp20	MD [auth Za] ND [auth Zb] OD [auth Zc] PD [auth Zd] QD [auth Ze] MD [auth Za], ND [auth Zb], OD [auth Zc], PD [auth Zd], QD [auth Ze], RD [auth Zf], SD [auth Zg], TD [auth Zh], UD [auth Zi], VD [auth Zj], WD [auth Zk], XD [auth Zl]	148	Frog virus 3	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative myristoylated protein 053R	AF [auth m1], BF [auth m2]	521	Frog virus 3	Mutation(s): 0
UniProt
Find proteins for Q6GZS3 (Frog virus 3 (isolate Goorha)) Explore Q6GZS3 Go to UniProtKB: Q6GZS3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6GZS3
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative myristylated membrane protein	CF [auth n1], DF [auth n2]	314	Frog virus 3	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Vp31	EF [auth pp]	139	Frog virus 3	Mutation(s): 0
UniProt
Find proteins for Q6GZU5 (Frog virus 3 (isolate Goorha)) Explore Q6GZU5 Go to UniProtKB: Q6GZU5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6GZU5
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Vp76	FF [auth rI] GF [auth rJ] HF [auth rK] IF [auth rL] JF [auth rM] FF [auth rI], GF [auth rJ], HF [auth rK], IF [auth rL], JF [auth rM], KF [auth rO], LF [auth rP], MF [auth rQ], NF [auth rR]	73	Frog virus 3	Mutation(s): 0
UniProt
Find proteins for Q6GZP9 (Frog virus 3 (isolate Goorha)) Explore Q6GZP9 Go to UniProtKB: Q6GZP9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6GZP9
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Vp10	OF [auth sa]	137	Frog virus 3	Mutation(s): 0
UniProt
Find proteins for Q6GZW5 (Frog virus 3 (isolate Goorha)) Explore Q6GZW5 Go to UniProtKB: Q6GZW5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6GZW5
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Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Vp70	PF [auth sb]	124	Frog virus 3	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Vp74	QF [auth tm]	362	Frog virus 3	Mutation(s): 0
UniProt
Find proteins for Q6GZQ1 (Frog virus 3 (isolate Goorha)) Explore Q6GZQ1 Go to UniProtKB: Q6GZQ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6GZQ1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	dev_6003
RECONSTRUCTION	RELION	4.0.0

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-21

Deposition Author(s):

Sandoval-Valencia, J.D.

Shah, P.N.M.

Stuart, D.

Fry, E.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	218482/Z/19/Z
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/V001329/1
CAMS Innovation Fund for Medical Sciences (CIFMS)	United Kingdom	2024-I2M-2-001-1

Revision History (Full details and data files)

Version 1.0: 2026-10-21
Type: Initial release

29KH | pdb_000029kh

Outer capsid of the ranavirus Frog Virus 3

Literature

Lessons for constructing and deconstructing giant viruses from the structure of Frog Virus 3

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

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

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)