PDB-2yo1: Salmonella enterica SadA 1049-1304 fused to GCN4 adaptors (SadAK9...

ID or keywords:

Entry

Database: PDB / ID: 2yo1

Title

Salmonella enterica SadA 1049-1304 fused to GCN4 adaptors (SadAK9- cfII)

Components

GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN

Keywords

MEMBRANE PROTEIN / HANS MOTIF / YADA-LIKE HEAD / YLHEAD / HEAD INSERT MOTIF / HIM / TRIMERIC AUTOTRANSPORTER ADHESIN / TAA / CHIMERA

Function / homology

Function and homology information

FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / amino acid biosynthetic process ...
Similarity search - Function

Biological species

SACCHAROMYCES CEREVISIAE (brewer's yeast)

SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Hartmann, M.D. / Hernandez Alvarez, B. / Lupas, A.N.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Complete Fiber Structures of Complex Trimeric Autotransporter Adhesins Conserved in Enterobacteria.
Authors: Hartmann, M.D. / Grin, I. / Dunin-Horkawicz, S. / Deiss, S. / Linke, D. / Lupas, A.N. / Hernandez Alvarez, B.

History

Deposition	Oct 20, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 12, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 9, 2013	Group: Database references
Revision 1.2	Mar 15, 2017	Group: Source and taxonomy
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2yo1.cif.gz	304.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2yo1.ent.gz	248.6 KB	Display	PDB format
PDBx/mmJSON format	2yo1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2yo1_validation.pdf.gz	454.4 KB	Display	wwPDB validaton report
Full document	2yo1_full_validation.pdf.gz	478.6 KB	Display
Data in XML	2yo1_validation.xml.gz	31.5 KB	Display
Data in CIF	2yo1_validation.cif.gz	42.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yo/2yo1 ftp://data.pdbj.org/pub/pdb/validation_reports/yo/2yo1	HTTPS FTP

-
Related structure data

Related structure data	2ynyC 2ynzC 2yo0C 2yo2C 2yo3C 1gcmS 1ce9 1dgc 1fav 1fmh 1gcl 1gk6 1gzl 1ihq 1ij0 1ij1 1ij2 1ij3 1kql 1ld4 1llm 1nkn 1piq 1rb4 1rb5 1rb6 1swi 1tmz 1unt 1unu 1unv 1unw 1unx 1uny 1unz 1uo0 1uo1 1uo2 1uo3 1uo4 1uo5 1w5g 1w5h 1w5i 1w5j 1w5k 1w5l 1ysa 1zii 1zij 1zik 1zil 1zim 1zta 2b1f 2b22 2bni 2cce 2ccf 2ccn 2d3e 2dgc 2wg5 2wg6 2wpq 2wpr 2wps 2wpy 2wpz 2wq0 2wq1 2wq2 2wq3 2zta 3k7z S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2xqh-1 2yo0-d 2yo0-1 5lsj-2 6eup-d 5lsj-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (9) #122 - Feb 2010 Enhanceosome similarity (4)

Deposited unit

A: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN

B: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN

C: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN

hetero molecules

102 kDa, 3 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)	82.030, 48.780, 135.830
Angle α, β, γ (deg.)	90.00, 105.10, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	1020 - 1097
2	1	1	1	B	1020 - 1097
3	1	1	1	C	1020 - 1097
1	1	2	1	A	1098 - 1107
2	1	2	1	C	1098 - 1107
1	1	3	1	A	1108 - 1136
2	1	3	1	B	1108 - 1136
3	1	3	1	C	1108 - 1136
1	1	4	5	A	1137 - 1148
2	1	4	5	B	1137 - 1148
3	1	4	5	C	1137 - 1148
1	1	5	1	A	1149 - 1159
2	1	5	1	B	1149 - 1159
3	1	5	1	C	1149 - 1159
1	1	6	1	A	1162 - 1200
2	1	6	1	B	1162 - 1200
3	1	6	1	C	1162 - 1200
1	1	7	5	B	1201 - 1219
2	1	7	5	C	1201 - 1219
1	1	8	5	B	1223 - 1240
2	1	8	5	C	1223 - 1240
1	1	9	1	A	1241 - 1304
2	1	9	1	B	1241 - 1304
3	1	9	1	C	1241 - 1304
1	1	10	1	A	1305 - 1341
2	1	10	1	B	1305 - 1341
3	1	10	1	C	1305 - 1341

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10

#1: Protein	GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN Mass: 34005.398 Da / Num. of mol.: 3 Fragment: RESIDUES 1049-1304 FUSED TO GCN4 ADAPTORS, RESIDUES 250-278 Mutation: YES Source method: isolated from a genetically manipulated source Details: N- AND C-TERMINAL IN-REGISTER FUSION TO GCN4 ADAPTORS Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast), (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03069, UniProt: Q8ZL64
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
Sequence details	C-TERMINAL HIS-TAG

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 49 % / Description: NONE
Crystal grow	Details: 15 % (V/V) BUTANEDIOL, 100 MM SODIUM ACETATE PH 4.2

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
Detector	Type: MARRESEARCH / Detector: CCD / Date: May 19, 2009
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.1→39.1 Å / Num. obs: 18792 / % possible obs: 96.9 % / Redundancy: 2.31 % / R_merge(I) obs: 0.1 / Net I/σ(I): 8.93
Reflection shell	Resolution: 3.1→3.28 Å / Redundancy: 2.35 % / R_merge(I) obs: 0.42 / Mean I/σ(I) obs: 2.35 / % possible all: 94.6

-
Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCM

1gcm

Resolution: 3.1→38.64 Å / Cor.coef. F_o:F_c: 0.901 / Cor.coef. F_o:F_c free: 0.851 / SU B: 55.961 / SU ML: 0.455 / Cross valid method: THROUGHOUT / ESU R Free: 0.58 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.32049	937	5 %	RANDOM
R_work	0.2648	-	-	-
obs	0.26752	17845	97.03 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 55.628 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.36 Å²	0 Å²	7.55 Å²
2-	-	2.28 Å²	0 Å²
3-	-	-	6.01 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→38.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5774	0	1	0	5775

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.021	5806
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3457
X-RAY DIFFRACTION	r_angle_refined_deg	1.324	1.922	7906
X-RAY DIFFRACTION	r_angle_other_deg	0.993	3	8570
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.613	5	816
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.7	26.923	247
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.773	15	886
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.986	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	984
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	6831
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1019
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0	1.5	4020
X-RAY DIFFRACTION	r_mcbond_other	0	1.5	1707
X-RAY DIFFRACTION	r_mcangle_it	0.002	2	6393
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.097	3	1786
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0.145	4.5	1513
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	346	tight positional	0.02	0.05
1	2	B	346	tight positional	0.02	0.05
1	3	C	346	tight positional	0.02	0.05
2	1	A	83	tight positional	0.03	0.05
3	1	A	314	tight positional	0.02	0.05
3	2	B	314	tight positional	0.02	0.05
3	3	C	314	tight positional	0.02	0.05
5	1	A	116	tight positional	0.03	0.05
5	2	B	116	tight positional	0.03	0.05
5	3	C	116	tight positional	0.03	0.05
6	1	A	434	tight positional	0.03	0.05
6	2	B	434	tight positional	0.03	0.05
6	3	C	434	tight positional	0.03	0.05
9	1	A	675	tight positional	0.05	0.05
9	2	B	675	tight positional	0.05	0.05
9	3	C	675	tight positional	0.05	0.05
10	1	A	355	tight positional	0.03	0.05
10	2	B	355	tight positional	0.04	0.05
10	3	C	355	tight positional	0.03	0.05
4	1	A	71	medium positional	0.4	0.5
4	2	B	71	medium positional	0.39	0.5
4	3	C	71	medium positional	0.57	0.5
7	1	B	113	medium positional	0.18	0.5
8	1	B	106	medium positional	0.14	0.5
4	1	A	85	loose positional	0.81	5
4	2	B	85	loose positional	0.86	5
4	3	C	85	loose positional	1.04	5
7	2	C	120	loose positional	0.24	5
8	2	C	106	loose positional	0.22	5
1	1	A	346	tight thermal	0	0.5
1	2	B	346	tight thermal	0	0.5
1	3	C	346	tight thermal	0	0.5
2	2	C	83	tight thermal	0	0.5
3	1	A	314	tight thermal	0	0.5
3	2	B	314	tight thermal	0	0.5
3	3	C	314	tight thermal	0	0.5
5	1	A	116	tight thermal	0	0.5
5	2	B	116	tight thermal	0	0.5
5	3	C	116	tight thermal	0	0.5
6	1	A	434	tight thermal	0	0.5
6	2	B	434	tight thermal	0	0.5
6	3	C	434	tight thermal	0	0.5
9	1	A	675	tight thermal	0	0.5
9	2	B	675	tight thermal	0	0.5
9	3	C	675	tight thermal	0	0.5
10	1	A	355	tight thermal	0	0.5
10	2	B	355	tight thermal	0	0.5
10	3	C	355	tight thermal	0	0.5
4	1	A	71	medium thermal	0	2
4	2	B	71	medium thermal	0	2
4	3	C	71	medium thermal	0	2
7	1	B	113	medium thermal	0	2
8	1	B	106	medium thermal	0	2
4	1	A	85	loose thermal	0	10
4	2	B	85	loose thermal	0	10
4	3	C	85	loose thermal	0	10
7	2	C	120	loose thermal	0	10
8	2	C	106	loose thermal	0	10

LS refinement shell

Resolution: 3.097→3.177 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.458	64	-
R_work	0.291	1211	-
obs	-	-	91.2 %

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	5.2935	-0.419	-0.7524	1.9543	-0.0061	2.828	0.3724	0.8654	0.4634	-0.396	-0.1718	-0.4931	-0.0724	0.7091	-0.2005	0.7625	0.047	0.0907	1.666	0.0198	0.6294	87.0706	0.2896	23.9724
2	14.4234	-0.8019	-7.2941	0.0542	0.4349	5.398	0.1241	-0.2458	-0.0119	-0.0394	-0.087	0.0863	-0.0744	0.3859	-0.0371	0.6908	0.0037	-0.1739	0.6321	-0.0729	0.4644	44.7698	-0.3871	45.5026
3	4.6381	0.4442	-1.3017	2.1645	-0.2728	1.9498	-0.0265	-0.3158	-0.1478	-0.0039	-0.053	-0.3403	0.0263	0.4917	0.0795	0.3374	-0.0262	-0.1098	0.1297	0.035	0.3549	-0.791	-0.0147	66.8365
4	13.5293	0.6223	-5.3507	0.1994	-0.267	3.1291	0.1312	-0.591	-0.1385	0.1822	-0.0568	0.3285	-0.1217	-0.4131	-0.0743	0.6749	0.0095	-0.0083	0.4109	0.0025	0.7709	-40.0025	-0.1756	81.363

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1020 - 1180
2	X-RAY DIFFRACTION	1	B	1020 - 1180
3	X-RAY DIFFRACTION	1	C	1020 - 1180
4	X-RAY DIFFRACTION	2	A	1181 - 1220
5	X-RAY DIFFRACTION	2	B	1181 - 1220
6	X-RAY DIFFRACTION	2	C	1181 - 1220
7	X-RAY DIFFRACTION	3	A	1221 - 1300
8	X-RAY DIFFRACTION	3	B	1221 - 1300
9	X-RAY DIFFRACTION	3	C	1221 - 1300
10	X-RAY DIFFRACTION	4	A	1301 - 1341
11	X-RAY DIFFRACTION	4	B	1301 - 1341
12	X-RAY DIFFRACTION	4	C	1301 - 1341

-
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