PDB-6cd2: Crystal structure of the PapC usher bound to the chaperone-adhesi...

ID or keywords:

Entry

Database: PDB / ID: 6cd2

Title

Crystal structure of the PapC usher bound to the chaperone-adhesin PapD-PapG

Components

Chaperone protein PapD
Outer membrane usher protein PapC
PapGII adhesin protein

Keywords

MEMBRANE PROTEIN/CHAPERONE / outer membrane usher / P pilus assembly / usher activation / MEMBRANE PROTEIN / MEMBRANE PROTEIN-CHAPERONE complex

Function / homology

Function and homology information

fimbrial usher porin activity / pilus assembly / pilus / : / cell outer membrane / cell wall organization / outer membrane-bounded periplasmic space / carbohydrate binding / cell adhesion / extracellular region / identical protein binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.7 Å

Authors

Omattage, N.S. / Deng, Z. / Yuan, P. / Hultgren, S.J.

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01AI029549	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01AI048689	United States
National Science Foundation (NSF, United States)	DGE-1745038	United States

Citation

Journal: Nat Microbiol / Year: 2018
Title: Structural basis for usher activation and intramolecular subunit transfer in P pilus biogenesis in Escherichia coli.
Authors: Omattage, N.S. / Deng, Z. / Pinkner, J.S. / Dodson, K.W. / Almqvist, F. / Yuan, P. / Hultgren, S.J.

History

Deposition	Feb 7, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 3, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 31, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Dec 12, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6cd2.cif.gz	462.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6cd2.ent.gz	380.5 KB	Display	PDB format
PDBx/mmJSON format	6cd2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6cd2_validation.pdf.gz	443.9 KB	Display	wwPDB validaton report
Full document	6cd2_full_validation.pdf.gz	455.3 KB	Display
Data in XML	6cd2_validation.xml.gz	41.5 KB	Display
Data in CIF	6cd2_validation.cif.gz	57.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cd/6cd2 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/6cd2	HTTPS FTP

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Related structure data

Related structure data	1j8sS 2vqiS 2wmpS 3l48S S: Starting model for refinement
Similar structure data	2grl-d 1zem-3 1zmo-d 3lg0-d 2xh2-d 21547 5owj-d 1ye6-4 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Chaperone protein PapD

B: PapGII adhesin protein

C: Outer membrane usher protein PapC

141 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)	204.303, 300.710, 100.515
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Chaperone protein PapD Mass: 25031.303 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: papD / Production host: Escherichia coli (E. coli) / References: UniProt: P15319
#2: Protein	PapGII adhesin protein Mass: 35519.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: Q47450
#3: Protein	Outer membrane usher protein PapC Mass: 80472.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PapC / Production host: Escherichia coli (E. coli) / References: UniProt: P07110*PLUS
Has protein modification	Y
Sequence details	The poly-UNK fragments in PapC sequence represent portions that the residue identities cannot be ...The poly-UNK fragments in PapC sequence represent portions that the residue identities cannot be determined from electron density. The full sequence of the entity is VEFNTDVLDAADKKNIDFTRFSEAGYVLPGQYLLDVIVNGQSISPASLQISFVEPALSGD KAEKKLPQACLTSDMVRLMGLTAESLDKVVYWHDGQCADFHGLPGVDIRPDTGAGVLRIN MPQAWLEYSDATWLPPSRWDDGIPGLMLDYNLNGTVSRNYQGGDSHQFSYNGTVGGNLGP WRLRADYQGSQEQSRYNGEKTTNRNFTWSRFYLFRAIPRWRANLTLGENNINSDIFRSWS YTGASLESDDRMLPPRLRGYAPQITGIAETNARVVVSQQGRVLYDSMVPAGPFSIQDLDS SVRGRLDVEVIEQNGRKKTFQVDTASVPYLTRPGQVRYKLVSGRSRGYGHETEGPVFATG EASWGLSNQWSLYGGAVLAGDYNALAAGAGWDLGVPGTLSADITQSVARIEGERTFQGKS WRLSYSKRFDNADADITFAGYRFSERNYMTMEQYLNARYRNDYSSREKEMYTVTLNKNVA DWNTSFNLQYSRQTYWDIRKTDYYTVSVNRYFNVFGLQGVAVGLSASRSKYLGRDNDSAY LRISVPLGTGTASYSGSMSNDRYVNMAGYTDTFNDGLDSYSLNAGLNSGGGLTSQRQINA YYSHRSPLANLSANIASLQKGYTSFGVSASGGATITGKGAALHAGGMSGGTRLLVDTDGV GGVPVDGGQVVTNRWGTGVVTDISSYYRNTTSVDLKRLPDDVEATRSVVESALTEGAIGY RKFSVLKGKRLFAILRLADGSQPPFGASVTSEKGRELGMVADEGLAWLSGVTPGETLSVN WDGKIQCQVNVPETAISDQQLLLPCTPQKLVPRGSHHHHHH The accession code of UniProt reference for the protein is P07110.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 5.12 Å³/Da / Density % sol: 75.99 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 50 mM sodium citrate pH 5.0-6.0, 50 mM lithium sulfate, 50 mM sodium sulfate and 7-14% PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 3.7→50 Å / Num. obs: 27152 / % possible obs: 98.5 % / Redundancy: 6 % / R_merge(I) obs: 0.122 / R_pim(I) all: 0.054 / R_rim(I) all: 0.134 / Net I/σ(I): 15.9
Reflection shell	Resolution: 3.7→3.83 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3048 / R_pim(I) all: 0.448 / % possible all: 92.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0103	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2VQI, 2WMP, 1J8S, 3L48

Resolution: 3.7→50.01 Å / Cor.coef. F_o:F_c: 0.832 / Cor.coef. F_o:F_c free: 0.791 / SU B: 91.949 / SU ML: 0.615 / Cross valid method: THROUGHOUT / ESU R Free: 0.77 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.32932	1384	5.1 %	RANDOM
R_work	0.28203	-	-	-
obs	0.28433	25768	80.96 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 135.172 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-10.34 Å²	0 Å²	0 Å²
2-	-	2.02 Å²	0 Å²
3-	-	-	8.32 Å²

Refinement step

Cycle: 1 / Resolution: 3.7→50.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8640	0	0	0	8640

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	8808
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	7649
X-RAY DIFFRACTION	r_angle_refined_deg	1.26	1.934	12064
X-RAY DIFFRACTION	r_angle_other_deg	0.927	3	17381
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.705	5	1247
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.743	24.441	322
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.562	15	1030
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.281	15	38
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	1388
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	10691
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2017
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	1.333	5.777	5021
X-RAY DIFFRACTION	r_mcbond_other	1.333	5.778	5020
X-RAY DIFFRACTION	r_mcangle_it	2.457	8.662	6257
X-RAY DIFFRACTION	r_mcangle_other	2.457	8.661	6258
X-RAY DIFFRACTION	r_scbond_it	0.746	5.297	3785
X-RAY DIFFRACTION	r_scbond_other	0.746	5.296	3786
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.518	8.043	5808
X-RAY DIFFRACTION	r_long_range_B_refined	6.472	52.353	33628
X-RAY DIFFRACTION	r_long_range_B_other	6.472	52.352	33629
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3.7→3.796 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.362	30	-
R_work	0.28	528	-
obs	-	-	23.12 %

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	2.6486	1.2083	-0.6217	6.9167	-2.1367	3.075	-0.522	-0.4581	1.0653	0.132	0.2487	0.4106	-0.4867	-0.2987	0.2733	1.3605	0.1945	-0.3193	0.9917	-0.177	0.5397	275.1344	21.8874	13.4424
2	5.18	0.9048	-1.767	0.8312	-1.2815	2.4725	-0.2459	0.3327	0.2761	0.2958	-0.0296	0.0028	-0.2377	-0.2026	0.2755	1.2321	0.0893	-0.1547	0.8692	-0.0953	0.2725	278.0749	14.4335	8.0378
3	18.6881	4.9854	-1.8454	2.3069	-0.9337	3.2764	0.42	-0.144	1.5693	0.4424	0.0222	0.1476	-0.5881	-0.3113	-0.4422	0.9922	0.1005	-0.1701	0.5635	-0.0254	0.6328	280.5827	16.2968	14.601
4	4.3816	0.0653	1.3629	3.9898	0.1283	6.5991	-0.2635	-0.4581	-0.165	0.8037	0.0295	0.3142	0.3028	-0.2854	0.2341	1.2736	0.105	-0.0181	0.9275	-0.125	0.4876	270.6949	4.5308	34.5083
5	1.6925	1.7617	-1.0664	6.9649	-2.2754	1.6679	-0.2085	-0.4621	-0.189	0.7625	0.2835	-0.8806	-0.1114	-0.0678	-0.0749	1.4569	0.2214	-0.18	1.0756	-0.0653	0.4623	276.05	7.3286	35.3349
6	11.6188	16.1327	-8.4278	26.8614	-15.8167	9.9262	0.0349	-0.3198	0.0856	0.0917	0.0987	0.1473	-0.0462	-0.1308	-0.1336	1.5479	0.0912	0.0513	1.1983	-0.2334	0.3519	267.7949	5.7769	42.3477
7	8.9127	-9.6759	7.1353	10.8933	-8.0224	5.9105	-0.271	-0.7454	0.3393	-0.1587	0.3989	0.1552	0.1128	-0.3375	-0.1278	1.1757	0.0943	-0.3735	0.9483	-0.457	1.0616	259.0969	39.6895	14.5027
8	4.6117	-3.1445	2.2179	2.3608	-2.3367	4.972	-0.5344	0.2352	0.4166	0.2839	-0.0959	-0.2819	-0.2853	0.2253	0.6303	1.3115	0.0925	-0.6457	0.5694	-0.4775	1.3018	257.7879	48.4354	5.832
9	0.6878	-1.329	1.2999	3.9371	-3.8018	5.0006	0.1943	-0.0528	0.4269	0.2759	-0.1465	0.1694	0.2932	0.2099	-0.0478	1.3543	0.3319	-0.1687	0.5329	-0.7077	1.6333	256.0449	45.5602	11.3044
10	4.2037	-6.712	3.8803	14.6845	-3.1858	7.247	-0.6599	-0.4785	1.1674	1.4845	-0.1943	-0.8818	-0.4364	-0.5149	0.8543	1.255	-0.1212	-0.2123	0.5966	-0.8225	1.3005	263.5739	44.766	14.754
11	9.2339	0.401	0.8555	1.8052	-2.7367	4.4554	0.1222	0.9482	0.3496	-0.0662	-0.3369	0.029	0.0853	0.7883	0.2147	1.1845	-0.0359	-0.3143	1.1561	-0.0271	0.7241	306.2378	21.289	15.6756
12	9.0493	-2.7548	-1.3061	1.99	1.6165	4.5266	-0.2832	-0.1076	-0.2895	0.1838	-0.0287	-0.2977	0.0436	0.0205	0.312	1.1542	0.0229	-0.2163	0.8696	0.0857	0.4666	299.5447	12.9606	17.7027
13	4.2989	-3.1621	2.9428	3.9845	-2.9302	2.3793	-0.5593	0.3332	0.9648	0.0743	-0.0699	-0.5064	-0.1698	0.1978	0.6292	1.3231	-0.1148	-0.244	0.8005	0.2001	0.8874	281.6063	31.7495	-8.8902
14	4.9286	-0.2469	0.1412	0.1459	-0.2382	0.4235	0.0305	0.445	0.8277	0.094	-0.0495	0.023	-0.3118	0.0414	0.0189	1.4813	0.1909	-0.4438	0.5987	0.0648	1.1283	250.3653	42.8194	-15.4764
15	2.2126	-0.8687	0.9383	0.5064	-0.1648	1.0293	-0.4674	0.6125	0.5731	0.1916	0.045	0.0793	0.124	0.3293	0.4225	1.0825	-0.1807	-0.5645	0.8879	0.6408	1.2139	231.6376	53.3459	-31.1479
16	5.3982	0.1553	1.3331	0.077	0.405	7.521	-0.5851	-0.0775	2.0241	0.2343	0.0563	-0.0119	-0.3693	-0.7557	0.5288	1.3596	0.4334	-0.6292	0.3126	0.1198	1.584	224.6703	63.5341	-15.8849
17	2.3595	0.2493	1.3418	1.7327	1.2632	1.5261	-0.3419	-0.4391	-0.0103	0.8563	0.4061	-0.2114	0.2396	0.1095	-0.0642	1.6745	0.2238	-0.3675	0.6655	0.4827	0.9474	231.1363	40.5919	-8.1197
18	10.234	1.7662	-1.4491	6.2826	0.1954	6.1477	0.0181	0.1128	0.6603	-0.3768	-0.3591	-0.0706	-0.322	-0.3734	0.341	1.0851	-0.0328	-0.1069	0.8006	0.0892	0.3554	276.1164	14.2384	-12.1513

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 27
2	X-RAY DIFFRACTION	2	A	28 - 95
3	X-RAY DIFFRACTION	3	A	96 - 125
4	X-RAY DIFFRACTION	4	A	126 - 160
5	X-RAY DIFFRACTION	5	A	161 - 199
6	X-RAY DIFFRACTION	6	A	200 - 215
7	X-RAY DIFFRACTION	7	B	1 - 35
8	X-RAY DIFFRACTION	8	B	36 - 111
9	X-RAY DIFFRACTION	9	B	112 - 167
10	X-RAY DIFFRACTION	10	B	168 - 197
11	X-RAY DIFFRACTION	11	B	198 - 226
12	X-RAY DIFFRACTION	12	B	227 - 316
13	X-RAY DIFFRACTION	13	C	1 - 88
14	X-RAY DIFFRACTION	14	C	89 - 173
15	X-RAY DIFFRACTION	15	C	174 - 417
16	X-RAY DIFFRACTION	16	C	418 - 588
17	X-RAY DIFFRACTION	17	C	592 - 723
18	X-RAY DIFFRACTION	18	C	724 - 808

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