PDB-9ztb: Crystal Structure of the macrodomain in the complex with suramin ...

ID or keywords:

Entry

Database: PDB / ID: 9ztb

Title

Crystal Structure of the macrodomain in the complex with suramin analog from Venezuelan equine encephalitis virus

Components

Polyprotein P1234

Keywords

HYDROLASE / Macrodomain / suramin / Venezuelan equine encephalitis virus (VEEV) / Hydratase / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID / Biopreparedness Research Virtual Environment (BRaVE)

Function / homology

Chem-SVR / :

Function and homology information

Biological species

Venezuelan equine encephalitis virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.67 Å

Authors

Kim, Y. / Stols, L. / Endres, M. / Babnigg, G. / Gora, N. / Hura, G. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of the macrodomain in the complex with suramin analog from Venezuelan equine encephalitis virus
Authors: Kim, Y. / Stols, L. / Endres, M. / Babnigg, G. / Gora, N. / Hura, G. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)

History

Deposition	Dec 23, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 12, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9ztb.cif.gz	171.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9ztb.ent.gz	109.9 KB	Display	PDB format
PDBx/mmJSON format	9ztb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	9zre 9zrf
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Polyprotein P1234

B: Polyprotein P1234

hetero molecules

36.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	39.471, 39.650, 56.060
Angle α, β, γ (deg.)	82.633, 69.389, 61.974
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

#1: Protein	Polyprotein P1234 / Non-structural polyprotein Mass: 17547.873 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Venezuelan equine encephalitis virus / Gene: NSP / Plasmid: mcsgv53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: M1JQW9
#2: Chemical	ChemComp-SVR / 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID / SURAMIN Mass: 1297.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅₁H₄₀N₆O₂₃S₆ / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.06 Å³/Da / Density % sol: 40.39 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.01 M sodium citrate, 33 % w/v PEG 6000

-
Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: 0.97934 / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 18, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 1.67→50 Å / Num. obs: 26769 / % possible obs: 82.3 % / Redundancy: 2.8 % / B_iso Wilson estimate: 13.43 Å² / CC_1/2: 0.988 / R_merge(I) obs: 0.107 / R_rim(I) all: 0.132 / Net I/σ(I): 8.7
Reflection shell	Resolution: 1.67→1.7 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.279 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1616 / CC_1/2: 0.603 / R_rim(I) all: 0.347 / % possible all: 95.7

-
Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.67→34.96 Å / SU ML: 0.2236 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 23.8119
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2523	1329	4.97 %
R_work	0.2033	25417	-
obs	0.2056	26746	82.21 %

Solvent computation

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

Displacement parameters

B_iso mean: 19.8 Å²

Refinement step

Cycle: LAST / Resolution: 1.67→34.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2385	0	86	229	2700

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0048	2550
X-RAY DIFFRACTION	f_angle_d	0.8622	3477
X-RAY DIFFRACTION	f_chiral_restr	0.0502	386
X-RAY DIFFRACTION	f_plane_restr	0.0051	439
X-RAY DIFFRACTION	f_dihedral_angle_d	13.5613	915

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 (%)
1.67-1.74	0.2854	169	0.2313	3267	X-RAY DIFFRACTION	94.79
1.74-1.82	0.2703	180	0.2136	3296	X-RAY DIFFRACTION	96.31
1.82-1.91	0.2525	201	0.1966	3170	X-RAY DIFFRACTION	93.43
1.91-2.03	0.2738	148	0.2123	3075	X-RAY DIFFRACTION	88.98
2.03-2.19	0.2798	162	0.1998	2774	X-RAY DIFFRACTION	80.73
2.19-2.41	0.2856	128	0.2147	2565	X-RAY DIFFRACTION	74.97
2.41-2.76	0.2662	111	0.2217	2444	X-RAY DIFFRACTION	71.19
2.76-3.47	0.222	112	0.2156	2242	X-RAY DIFFRACTION	64.85
3.48-34.96	0.2143	118	0.1742	2584	X-RAY DIFFRACTION	74.72

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	4.21384586997	-0.386175233277	1.96189024631	0.436228537801	-0.919906000633	2.45429019995	-0.132630036837	-0.551514549005	0.585180027842	0.0807514522605	-0.00441820039154	0.0348329014309	-0.370494950088	-0.344325206859	0.0783084044032	0.10976656585	0.0371710527079	-0.0230429287495	0.225324571117	-0.0652561001648	0.311370093259	-6.27874961457	16.7055062501	-17.1754051833
2	3.07318249076	0.523916076675	1.55247178489	1.62689423244	1.64967119421	4.6245157839	-0.0160957580997	-0.230986458435	0.381540370536	0.00679611997699	-0.0579233034506	-0.0745490098596	-0.327545986411	-0.155769252433	0.0754335246445	0.0918810869747	0.0140653591084	-0.0115638760585	0.124809366026	-0.0271089878274	0.191898417272	1.71729312804	20.7385562445	-11.2232581745
3	0.288435735931	0.0415987689401	0.0574315622966	0.215527806827	0.0519493194511	0.0783343103952	-0.0199517766889	0.00843513877753	0.0379657841503	-0.0107930701564	-0.00208935486916	0.0599996403632	-0.0239280548352	-0.0311506505552	-0.0617051895785	0.0230246815643	-0.000764305356209	0.00913867634011	0.151136311998	-0.00665287333933	0.19737228464	1.1208413981	7.59014571975	-22.7998670062
4	0.709731901453	-0.119100675055	-0.386549758062	2.35432398436	-1.07132300317	0.852290832347	0.0296695685417	-0.0802089988801	0.108794749095	0.0623532415801	-0.101975655269	-0.184299283618	-0.0669210967698	0.147416021754	0.0359734541493	0.0178362746662	-0.00313418653405	-0.0177670685171	0.161239843878	-0.00396611850305	0.265858118959	11.2735733221	18.0134310982	-12.8753686515
5	1.53339392429	0.421313307562	-0.139894173512	0.56059162831	-0.134080767238	0.383856776584	0.0641288285572	0.0344323748957	-0.0731963628078	0.0254314634866	0.00453258445216	-0.0773704138362	0.0612363272189	0.0557526577478	0.0631015469044	0.0374741799264	0.0123994634056	0.00162254915183	0.147189403135	-0.00554753498359	0.207363166995	5.59981724698	1.62600961259	-17.7100566908
6	2.81911715908	-1.18096965466	0.471219202758	0.503188782627	-0.0635433698289	1.81183399195	-0.0592105592341	-0.107717110178	-0.126459794262	0.061101010955	0.0765953112086	-0.068058114627	0.00214360495483	0.0714120567881	0.0307894187484	0.0640920057857	0.00199284827151	0.000809615746973	0.208265436647	-0.0298948836642	0.263152688565	12.0331312167	8.29083560203	-10.1328437474
7	2.94020605777	-1.00560688766	-1.23337391126	1.37169204162	-0.319937631652	3.18516105886	0.0933293650279	-0.0516343668351	-0.153277047916	0.0465974868033	0.0188741510866	-0.14388481227	0.0386542990853	0.201882303881	-0.0297892368327	0.130326053856	0.0439821958597	-0.0357737440529	0.327399599788	0.000198907889131	0.319333093003	16.3987922377	-1.68025709773	-11.1157513126
8	5.57461839207	2.02721384283	-2.43818748852	2.15310146957	-1.62994626478	3.38453549488	0.00444534171429	0.224402329216	-0.287243004807	-0.0129312830904	0.0445290662313	0.153370590273	0.218213346916	-0.200785387928	4.18681577161E-6	0.0989235597264	-0.00712333618906	0.0281967176265	0.175182968709	-0.0570894166107	0.294801515659	-8.88223928758	-21.7714229452	11.07781078
9	1.54945853367	-0.720739706107	0.170566142507	1.69846986304	1.29753444225	2.71281188615	0.0621380257537	0.222482516723	0.147522113239	-0.173170934479	-0.0341639918702	-0.184453116288	-0.231114449965	0.245233567852	-0.0871121737841	0.0881816500465	0.000504207385506	0.0070418445591	0.239768896428	0.038279430918	0.241364287507	-5.45105796452	-4.96331665302	8.5298531417
10	5.12793423391	-4.50730190627	-2.16083044949	4.30367262864	3.28560854967	6.83079375261	0.264213646581	0.39256023494	0.515832540195	-0.393655828918	-0.312605056129	-0.441754726571	-0.0104052826136	0.0701607140988	0.0312084641071	0.243777512703	0.0340442799914	0.0749861353931	0.30344915449	0.120571976325	0.348065428087	-7.44084200665	-0.0559815581847	3.43456643118
11	1.0798111094	-0.536739589803	0.648495120041	0.390637999719	-0.182815272734	0.572299157508	-0.00204033750843	0.044877667029	0.231245065452	-0.0482822074201	-0.0341852630313	-0.00210424856447	-0.115874828974	-0.168056103391	0.0707446294991	0.052515311823	0.0377929202191	0.00279379396302	0.194203695148	0.00463193862596	0.250163654009	-10.0952307879	-0.191093269979	14.4108371321
12	0.965665980172	0.0602988651145	0.223590232935	0.0541787397628	0.0400722830965	0.113724361098	0.0126545536889	-0.067946408335	0.00203758593011	0.0215220126065	-0.0323744151847	-0.0296133631248	-0.0216710191062	-0.00102878233417	-0.0302087082442	-0.0921202022169	0.00824596131913	0.0125621706307	0.146097746605	-0.0233118732997	0.242049138832	-1.24069335781	-8.05907594378	23.3902263412
13	3.79795827267	-1.04988633829	-1.67751714133	0.701888062889	0.48894475638	1.67046773664	-0.0632130869423	0.167125818494	-0.209252582284	0.00733559735673	-0.0168325216041	0.0990007363816	0.132681536335	-0.13250187725	0.0793157545161	0.0089081647936	-0.00564053111194	0.00468205593639	0.265688784789	-0.0103421502964	0.189011552266	-15.0370995345	-12.3069990508	13.525543185
14	1.22411315078	0.265832872406	-0.197738042106	0.505335626689	-0.197507754581	0.55943630192	0.00913064903205	0.0146063450934	-0.0924954097601	0.00141600088681	0.0335969427422	0.0158895245258	0.0579423862406	0.0534355775012	0.038494163588	-0.0171199224175	-0.000166127868231	0.0087221733175	0.153169280453	-0.00202486474686	0.251523220387	1.88622316607	-14.7395356084	18.2606219065
15	2.84114874864	-1.04509409089	-1.40627663584	2.06413689403	0.232341238054	3.60891990976	0.0914645496011	0.128352987248	0.185666142211	-0.109208969234	0.0233949086287	-0.0460351533511	0.012286185398	-0.0217231579614	-0.14131772107	0.0770804167469	-0.00395727537836	-0.00917122001188	0.173052656118	-0.0320372870702	0.227592492262	-6.84057592089	-17.3969696106	10.5979795712
16	3.92411712707	0.461385753874	1.44871906683	2.74304890291	-2.1182755111	4.70162995075	0.205622597589	0.487644084669	-0.360335644235	-0.116508054193	0.181007481355	0.111221745302	0.372446453139	-0.0802189857164	-0.361676082094	0.221664100597	0.0158037034577	0.00163867985496	0.202938708047	-0.063328665114	0.311932101862	0.43219054391	-25.67411833	11.5395031084
17	2.38741142075	-0.939272453601	1.53707271982	0.787557137178	-0.038589544903	1.75471078627	0.0436879440602	-0.15927162681	0.12249166189	0.0218660452131	0.0643585547866	-0.00640947660419	-0.0163584254682	0.0921376685393	-0.0713531508728	0.081524357417	0.00658389650219	-0.0126949470331	0.161078859641	0.0190901850746	0.315039218487	16.8018987193	7.98686894785	-10.6185036331
18	3.46367080426	1.11006147106	2.66495804589	2.44404107848	1.17073383	3.10012523031	-0.16603398916	-0.406393833537	0.115927834222	0.223415390733	0.0222411387359	0.111994320601	0.0244539222307	-0.298712011304	0.109918576353	0.109179147387	0.0166301250498	0.0290439230223	0.201821526699	-0.0326012100022	0.183200824742	2.23194435694	12.7911602781	-7.79152997362
19	1.46706755729	-1.04628576129	0.991252961151	5.03088556383	-4.36518980745	3.79437085996	-0.203141596626	-0.142360670392	0.0315430239038	0.491810495777	0.0316169149143	0.0483120714087	-0.131302209256	-0.818396786657	0.170888866279	0.278828045896	-0.0219703248949	0.00560505934464	0.62789263549	-0.234040245788	0.313894138344	-2.72565135402	17.9102439386	-2.12304767426

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 'B' and (resid 45 through 54 )	B	C	45 - 54	38 - 47
2	2	chain 'B' and (resid 55 through 68 )	B	C	55 - 68	48 - 61
3	3	chain 'B' and (resid 69 through 98 )	B	C	69 - 98	62 - 91
4	4	chain 'B' and (resid 99 through 107 )	B	C	99 - 107	92 - 100
5	5	chain 'B' and (resid 108 through 134 )	B	C	108 - 134	101 - 127
6	6	chain 'B' and (resid 135 through 145 )	B	C	135 - 145	128 - 138
7	7	chain 'B' and (resid 146 through 160 )	B	C	146 - 160	139 - 153
8	8	chain 'A' and (resid 0 through 8 )	A	A	0 - 8	1 - 9
9	9	chain 'A' and (resid 9 through 32 )	A	A	9 - 32	10 - 33
10	10	chain 'A' and (resid 33 through 44 )	A	A	33 - 44	34 - 45
11	11	chain 'A' and (resid 45 through 68 )	A	A	45 - 68	46 - 69
12	12	chain 'A' and (resid 69 through 98 )	A	A	69 - 98	70 - 99
13	13	chain 'A' and (resid 99 through 107 )	A	A	99 - 107	100 - 108
14	14	chain 'A' and (resid 108 through 134 )	A	A	108 - 134	109 - 135
15	15	chain 'A' and (resid 135 through 145 )	A	A	135 - 145	136 - 146
16	16	chain 'A' and (resid 146 through 159 )	A	A	146 - 159	147 - 160
17	17	chain 'B' and (resid 0 through 8 )	B	C	0 - 8	1 - 9
18	18	chain 'B' and (resid 9 through 36 )	B	C	9 - 36	10 - 29
19	19	chain 'B' and (resid 37 through 44 )	B	C	37 - 44	30 - 37

-
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