PDB-9oik: Structure of S. Typhimurium 14028 Gifsy-1 prophage HepS bound to ...

ID or keywords:

Entry

Database: PDB / ID: 9oik

Title

Structure of S. Typhimurium 14028 Gifsy-1 prophage HepS bound to bacteriophage lambda J Tail Tip

Components

HepS-H105A
J tail tip

Keywords

VIRAL PROTEIN / tail tip protein / HepS / HEPN / tRNase

Function / homology

Function and homology information

symbiont genome ejection through host cell envelope, long flexible tail mechanism / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / viral tail assembly / septin ring ...
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028 (bacteria)

Escherichia phage Lambda (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.857 Å

Authors

Sargen, M.R. / Antine, S.P. / Grabe, G.J. / Antonellis, G. / Ragucci, A.E. / Kranzusch, P.J. / Helaine, S.A.

Funding support

United States, 1items

Citation

Journal: Nature / Year: 2026
Title: A prophage-encoded abortive infection protein preserves host and prophage spread
Authors: Sargen, M.R.

History

Deposition	May 6, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 28, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9oik.cif.gz	258.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9oik.ent.gz	170.2 KB	Display	PDB format
PDBx/mmJSON format	9oik.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oi/9oik ftp://data.pdbj.org/pub/pdb/validation_reports/oi/9oik	HTTPS FTP

-
Related structure data

Related structure data	9oijC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#73 - Jan 2006 Topoisomerase similarity (1) #161 - May 2013 Ricin similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: HepS-H105A

B: HepS-H105A

C: J tail tip

D: J tail tip

86.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: HepS-H105A

B: HepS-H105A

C: J tail tip

D: J tail tip

A: HepS-H105A

B: HepS-H105A

C: J tail tip

D: J tail tip

defined by author&software
Evidence: assay for oligomerization, Mass Photometry
174 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	78.190, 93.878, 92.456
Angle α, β, γ (deg.)	90.000, 110.811, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Components on special symmetry positions

ID	Model	Components
1	1	A-313- HOH
2	1	B-310- HOH
3	1	B-457- HOH

#1: Protein	HepS-H105A Mass: 25496.336 Da / Num. of mol.: 2 / Mutation: H105A Source method: isolated from a genetically manipulated source Details: MGS N-terminal linker and C-terminal FLAG tag. Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028 (bacteria) Gene: STM14_3211 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): LOBSTR- -RIL / References: UniProt: A0A0F6B549
#2: Protein	J tail tip / Central tail fiber / Host specificity protein J / gpJ protein Mass: 17916.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal 10X-His followed by Smt3p tag followed by bacteriophage lambda J tail tip protein residues I902 to L933.,N-terminal 10X-His followed by Smt3p tag followed by bacteriophage lambda ...Details: N-terminal 10X-His followed by Smt3p tag followed by bacteriophage lambda J tail tip protein residues I902 to L933.,N-terminal 10X-His followed by Smt3p tag followed by bacteriophage lambda J tail tip protein residues I902 to L933. Source: (gene. exp.) Escherichia phage Lambda (virus) / Gene: SMT3, YDR510W, D9719.15, J, lambdap21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): LOBSTR- -RIL / References: UniProt: Q12306, UniProt: P03749
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 1.83 Å³/Da / Density % sol: 32.66 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2 M Sodium Acetate, 16% PEG 4000, 0.1 M Tris pH 8.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97935 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2025 Details: Horizontal pre-focus bimorph mirror & KB bimorph mirrors
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97935 Å / Relative weight: 1
Reflection	Resolution: 1.857→43.21 Å / Num. obs: 102985 / % possible obs: 100 % / Redundancy: 4.4 % / B_iso Wilson estimate: 28.28 Å² / CC_1/2: 0.996 / Net I/σ(I): 6.7
Reflection shell	Resolution: 1.857→1.889 Å / R_merge(I) obs: 1.04 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 50821 / CC_1/2: 0.387 / R_pim(I) all: 0.547

-
Processing

Software

Name	Version	Classification
PHENIX	1.21.1_5286	refinement
XDS	Jun 30, 2024 (BUILT 20241002)	data reduction
autoPROC	1.0.5 (20240123)	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.857→43.21 Å / SU ML: 0.2328 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.7076
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2093	2530	4.81 %
R_work	0.183	50095	-
obs	0.1842	102985	99.93 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 33.48 Å²

Refinement step

Cycle: LAST / Resolution: 1.857→43.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3715	0	0	524	4239

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0069	3778
X-RAY DIFFRACTION	f_angle_d	0.8076	5100
X-RAY DIFFRACTION	f_chiral_restr	0.0526	594
X-RAY DIFFRACTION	f_plane_restr	0.0067	649
X-RAY DIFFRACTION	f_dihedral_angle_d	12.8214	1403

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.86-1.89	0.3082	140	0.2981	2717	X-RAY DIFFRACTION	99.55
1.89-1.93	0.3394	140	0.2705	2772	X-RAY DIFFRACTION	99.9
1.93-1.97	0.2738	155	0.2614	2825	X-RAY DIFFRACTION	99.87
1.97-2.02	0.2612	111	0.2325	2738	X-RAY DIFFRACTION	99.93
2.02-2.07	0.2456	138	0.2279	2767	X-RAY DIFFRACTION	100
2.07-2.13	0.2827	140	0.2137	2789	X-RAY DIFFRACTION	99.9
2.13-2.19	0.2637	175	0.2055	2770	X-RAY DIFFRACTION	99.97
2.19-2.26	0.2603	147	0.1959	2768	X-RAY DIFFRACTION	99.97
2.26-2.34	0.2215	124	0.1968	2777	X-RAY DIFFRACTION	100
2.34-2.43	0.2122	124	0.1905	2821	X-RAY DIFFRACTION	99.86
2.43-2.54	0.2044	140	0.1779	2766	X-RAY DIFFRACTION	100
2.54-2.68	0.2033	139	0.1805	2759	X-RAY DIFFRACTION	99.93
2.68-2.85	0.2011	137	0.1806	2779	X-RAY DIFFRACTION	100
2.85-3.06	0.2248	144	0.1841	2814	X-RAY DIFFRACTION	100
3.06-3.37	0.2059	126	0.1758	2809	X-RAY DIFFRACTION	99.97
3.37-3.86	0.1887	155	0.1593	2775	X-RAY DIFFRACTION	99.97
3.86-4.86	0.1608	140	0.1437	2817	X-RAY DIFFRACTION	99.97
4.86-43.21	0.1778	155	0.1762	2832	X-RAY DIFFRACTION	99.9

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.597821455125	0.325715215665	-0.00808918836227	0.73606187976	-0.14830224275	0.63777207554	-0.0172068886748	-0.0061806418851	0.0354632938934	0.0174093381572	0.0629202939517	0.0586353700156	-0.0231500760446	-0.0162754491742	0.00753510404	0.188998942539	0.0723566541682	-2.422426719E-5	0.192770502513	0.0291334015189	0.206339371486	14.0041070809	23.0539018808	21.2393785314
2	0.256064514298	0.134311244994	-0.22890871831	0.919624212892	0.240785088671	0.407291003421	0.142612821764	-0.249363669278	-0.0109959920464	0.251952590313	-0.238763641635	0.0193338644674	0.104463708547	-0.021294386759	0.00229102166245	0.251252743395	0.039569751061	0.00801864121969	0.260017544535	0.00840562926866	0.209702127815	18.4005421715	3.33858190749	27.8600685644
3	0.204159737018	-0.241022173319	-0.0159492099705	0.312797286048	0.118351548897	0.110321130217	0.0921704988055	-0.0485330814403	0.00817729509575	0.311783562146	0.121084980355	-0.183086789328	0.328036323885	0.0846556504452	0.000340759587514	0.244049282251	0.0172515024521	-0.0267089899241	0.302215277905	0.040448259654	0.311742478175	29.9428787786	16.7514318876	34.0478430272
4	1.35848369581	-0.0766668534944	0.0355603511019	0.699994023493	-0.328511385037	1.41790845824	-0.0366847935539	0.14833860708	0.127392477759	-0.15679001967	0.00722246231116	-0.16848063039	-0.363720269506	0.420970005054	0.000100778039926	0.213582760785	-0.000573317833862	0.0238578018756	0.242952536903	0.0692275116437	0.271724726945	28.5000807041	23.842524659	22.9639879337
5	0.264462337833	-0.243395813752	0.276687471391	0.370911247373	0.0926538476607	1.13009753453	-0.0138091943831	-0.0355315838384	-0.0556793687381	-0.0633462765873	0.091871863397	-0.351820060817	-0.164811084989	0.551526409652	0.153960489145	0.368672984214	0.023169489407	0.0227777649607	0.305884897082	-0.0236723264114	0.242980602184	11.380418668	26.2403878385	5.36017080975
6	0.545360520612	0.168225647656	0.268340811699	0.557781880135	0.475394494992	0.413440749351	-0.00767828764764	-0.0975780008538	-0.0197564484917	0.152543535766	-0.0556389757656	-0.0232693884797	0.216098132466	-0.0164090875889	-0.00638865489242	0.277509231538	0.0783525470543	0.0112244541079	0.190581930802	-0.0148633252293	0.186022496906	28.4819800211	-21.8972723274	26.3526292072
7	0.692955658641	0.0755539324328	0.394042657302	0.96682906941	0.636400404894	0.580494111518	0.111253475669	-0.163520416703	-0.00902576309349	0.350947484939	0.0159042368717	-0.179671065138	0.0549549928656	-0.0242284647593	0.10466909848	0.253016806548	0.0868608037443	-0.0433396182053	0.241521268873	-0.020600626708	0.193221094566	26.3345392871	-4.25382586831	27.7971619717
8	0.683008255887	-0.424907579243	-0.339555004306	0.525666557829	-0.054765643283	0.390304484085	-0.0331654745691	-0.0774884350725	-0.00590302821205	0.260034114585	0.0372755916995	0.260911138261	-0.0550386448061	-0.530128175333	0.000656568573725	0.280297006929	-0.0266523206848	0.0427616350994	0.291269604512	-0.0398803145313	0.250519857673	12.298001762	-21.6867157566	34.4383336034
9	0.936401556136	0.421334607307	-0.657597215756	0.881926965704	0.0856998944136	0.663856641158	-0.129915695519	0.329551721604	-0.0715840128364	-0.24143713795	0.0162980360962	0.105555279612	0.376031473758	-0.458676696417	-0.0319808483598	0.299563853702	-0.00662699712919	-0.00870516489036	0.266324955439	-0.0849146736365	0.235142470098	16.2431879473	-26.180771986	16.4972583846
10	0.383288671425	0.457709829844	0.0224368227747	0.466395382952	0.211520489446	0.657996357153	-0.0172186139133	-0.00234265131838	-0.074679678972	0.035360699212	-0.164715250141	0.0145970761254	0.0975922904117	-0.110840789189	-0.121660325012	0.226354697255	0.0567167616633	0.0160918271949	0.199104831723	-0.0321459467323	0.217307295385	24.4326323358	-21.4027675869	18.8243124306
11	0.0975804481806	0.10882336872	0.14707123161	0.112428280405	0.150973696814	0.321325715693	-0.380647349829	-0.0351850668394	0.00845945077332	-0.53491870248	0.0529336057304	-0.331342298446	-0.116522019011	0.5503155852	0.0181965300806	0.544873601269	-0.0153182510274	-0.0585425256662	0.27124634691	0.114949252446	0.520950832975	21.0544083323	30.7191201441	14.8902351945
12	0.588432451231	0.0770208711636	0.312328886877	1.02148339506	0.783543131454	0.71844604537	-0.300447528346	-0.428778758287	0.0224347339847	0.103118421774	-0.094187461681	-0.121612868759	0.33297782991	0.199452387505	-0.176255113055	0.231658708087	0.0897466104387	-0.0119642958026	0.226546192639	0.0495253254498	0.212293249396	9.71581998976	22.8170328247	15.7885738199
13	0.00503198834851	-0.0208545655152	0.0116964330257	0.0550796710288	-0.00628564189966	0.0593657257251	0.23622163711	0.157813171543	-0.0727346059274	-0.119803430981	-0.074387084	-0.449362083143	0.148129828014	-0.219993782793	0.000378923564688	0.379935848349	0.00183166709005	-0.00584034198638	0.35300248688	0.0679343006638	0.315978416602	18.3454288795	22.093067994	4.22859114907
14	0.531555455475	0.154595424015	-0.293314244701	0.0484916757963	-0.12634271526	0.616261003344	-0.0843612422869	0.376656329589	-0.303423361149	-0.867941429807	-0.12442309523	0.0329442984579	0.236791979437	-0.381370790343	-0.298555538265	0.568587078916	0.0165652013813	-0.056224300597	0.267387118355	-0.137173959866	0.331176493847	21.5724728472	-32.6395634707	12.1772829115
15	0.152304208361	0.0497573377568	-0.211499811771	0.0168024343202	-0.0663160667669	0.285490363258	-0.160156843558	-0.0424443195932	0.284077459711	-0.141106569942	-0.0486599485112	0.040812753642	-0.0294711728262	-0.127141291214	-0.00295337564721	0.238622048598	0.0610537634654	-0.0118753455155	0.182879806693	-0.0292918445358	0.218723471085	35.252837627	-23.6010047853	15.1010691491
16	0.887527125269	-0.509182677955	0.392680705065	1.70354171599	-0.657359907182	0.320564827884	0.0561451091626	0.92516573626	0.156270659852	-0.714036556073	-0.563025457427	-0.255230148671	-0.0199175405605	-0.123634842786	-0.0729251844689	0.358302982833	0.043104013496	0.00547543981121	0.358229571934	-0.0265216284686	0.220003848026	25.1396270681	-22.4992997888	3.81742039019

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 0 through 58 )	A	A	0 - 58	1 - 59
2	2	chain 'A' and (resid 59 through 86 )	A	A	59 - 86	60 - 87
3	3	chain 'A' and (resid 87 through 105 )	A	A	87 - 105	88 - 106
4	4	chain 'A' and (resid 106 through 194 )	A	A	106 - 194	107 - 193
5	5	chain 'A' and (resid 195 through 219 )	A	A	195 - 219	194 - 218
6	6	chain 'B' and (resid 9 through 58 )	B	B	9 - 58	1 - 50
7	7	chain 'B' and (resid 59 through 86 )	B	B	59 - 86	51 - 78
8	8	chain 'B' and (resid 87 through 125 )	B	B	87 - 125	79 - 117
9	9	chain 'B' and (resid 126 through 164 )	B	B	126 - 164	118 - 154
10	10	chain 'B' and (resid 165 through 207 )	B	B	165 - 207	155 - 197
11	11	chain 'C' and (resid 902 through 915 )	C	C	902 - 915	1 - 8
12	12	chain 'C' and (resid 916 through 925 )	C	C	916 - 925	9 - 18
13	13	chain 'C' and (resid 926 through 932 )	C	C	926 - 932	19 - 25
14	14	chain 'D' and (resid 902 through 915 )	D	D	902 - 915	1 - 14
15	15	chain 'D' and (resid 916 through 925 )	D	D	916 - 925	15 - 24
16	16	chain 'D' and (resid 926 through 933 )	D	D	926 - 933	25 - 32

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi