PDB-9fm0: Human antibody (Fab) and P. aeruginosa (T3SS) protein PcrV-fragme...

ID or keywords:

Entry

Database: PDB / ID: 9fm0

Title

Human antibody (Fab) and P. aeruginosa (T3SS) protein PcrV-fragment complex

Components

Human Fab Heavy Chain (FabHC) V-region
Human Fab Light Chain (FabLC) V-region
Type III secretion protein PcrV

Keywords

IMMUNE SYSTEM / HUMAN ANTIBODIES / TYPE III SECRETION SYSTEM / PCRV / VIRULENCE / PSEUDOMONAS / BACTERIAL INFECTION / antimicrobials / anti-virulence / mAb / AMR

Function / homology

Low calcium response V antigen / Virulence-associated V antigen superfamily / V antigen (LcrV) protein / type III protein secretion system complex / protein secretion by the type III secretion system / extracellular space / DI(HYDROXYETHYL)ETHER / Type III secretion protein PcrV

Function and homology information

Biological species

Homo sapiens (human)

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.56 Å

Authors

Desveaux, J.M. / Contreras Martel, C. / Dessen, A.

Funding support

France, 1items

Citation

Journal: To Be Published
Title: Human antibodies that target the Type III Secretion System of Pseudomonas aeruginosa inhibit translocon function and cytotoxicity
Authors: Desveaux, J.M. / Faudry, E. / Contreras-Martel, C. / Cretin, F. / Dergan-Dylon, S. / Amen, A. / Bally, I. / Tardivy-Casemajor, V. / Chenavier, F. / Caspar, Y. / Attree, I. / Dessen, A. / Poignard, P.

History

Deposition	Jun 5, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 18, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9fm0.cif.gz	573.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9fm0.ent.gz	363.5 KB	Display	PDB format
PDBx/mmJSON format	9fm0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fm/9fm0 ftp://data.pdbj.org/pub/pdb/validation_reports/fm/9fm0	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.15151/ESRF-DC-1732137788 / Data set type: diffraction image data / Metadata reference: 10.15151/ESRF-ES-1131971883

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Human Fab Heavy Chain (FabHC) V-region

B: Human Fab Heavy Chain (FabHC) V-region

C: Human Fab Light Chain (FabLC) V-region

D: Human Fab Light Chain (FabLC) V-region

E: Type III secretion protein PcrV

F: Type III secretion protein PcrV

hetero molecules

124 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Human Fab Heavy Chain (FabHC) V-region

C: Human Fab Light Chain (FabLC) V-region

E: Type III secretion protein PcrV

hetero molecules

defined by author&software
Evidence: gel filtration, (ab/c) and (ab/c)2 can be observed under gel filtration
61.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Human Fab Heavy Chain (FabHC) V-region

D: Human Fab Light Chain (FabLC) V-region

F: Type III secretion protein PcrV

hetero molecules

defined by author&software
61.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.582, 92.308, 105.220
Angle α, β, γ (deg.)	90.000, 104.828, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	1	A	1 - 225
2	1	1	A	1 - 225
3	2	2	A	1 - 214
4	2	2	A	1 - 214
5	3	3	A	122 - 249
6	3	3	A	122 - 249

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

-
Protein , 1 types, 2 molecules EF

#3: Protein	Type III secretion protein PcrV Mass: 14359.030 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-ter TAG from residue K17 / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: pcrV, PA1706 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G3XD49

-
Antibody , 2 types, 4 molecules ABCD

#1: Antibody	Human Fab Heavy Chain (FabHC) V-region Mass: 23748.467 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: MEMORY B / Cell line (production host): HEK293F / Organ (production host): KIDNEY / Production host: Homo sapiens (human)
#2: Antibody	Human Fab Light Chain (FabLC) V-region Mass: 23320.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: MEMORY B / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / Tissue (production host): KIDNEY

-
Non-polymers , 3 types, 402 molecules

#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₁₀O₃ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.25 Å³/Da / Density % sol: 62.2 % / Description: Plates
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Micro-seeding, 0.1 M Sodium Acetate pH 5, 25% PEG 1000, 0.001M ZnCl2 PH range: 4.5-5.0

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 15, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.965459 Å / Relative weight: 1
Reflection	Resolution: 2.559→49.21 Å / Num. obs: 52157 / % possible obs: 99.5 % / Redundancy: 3.38 % / B_iso Wilson estimate: 45.86 Å² / CC_1/2: 0.977 / R_sym value: 0.2 / Net I/σ(I): 5.02
Reflection shell	Resolution: 2.56→2.71 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 0.72 / Num. unique obs: 8128 / CC_1/2: 0.312 / R_sym value: 1.53 / % possible all: 99.2

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS	20220820	data reduction
XSCALE	20220820	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.56→49.21 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.92 / SU B: 27.515 / SU ML: 0.264 / Cross valid method: FREE R-VALUE / ESU R: 0.44 / ESU R Free: 0.262
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.237	2086	3.999 %
R_work	0.2097	50071	-
all	0.211	-	-
obs	-	52157	99.54 %

Solvent computation

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

Displacement parameters

B_iso mean: 46.739 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.306 Å²	0 Å²	-0.474 Å²
2-	-	-0.233 Å²	-0 Å²
3-	-	-	0.156 Å²

Refinement step

Cycle: LAST / Resolution: 2.56→49.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8596	0	46	392	9034

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	8835
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	8148
X-RAY DIFFRACTION	r_ext_dist_refined_b	0.002	0.01	470
X-RAY DIFFRACTION	r_angle_refined_deg	1.266	1.802	11978
X-RAY DIFFRACTION	r_angle_other_deg	0.456	1.741	18847
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.449	5	1133
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.495	5	45
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.536	10	1417
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.825	10	361
X-RAY DIFFRACTION	r_chiral_restr	0.055	0.2	1337
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	10459
X-RAY DIFFRACTION	r_gen_planes_other	0.012	0.02	2021
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	1507
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	7397
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	4226
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	4589
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.243	0.2	265
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.102	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.109	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.183	0.2	64
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.128	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	2.154	2.908	4536
X-RAY DIFFRACTION	r_mcbond_other	2.152	2.908	4536
X-RAY DIFFRACTION	r_mcangle_it	3.543	5.215	5660
X-RAY DIFFRACTION	r_mcangle_other	3.543	5.215	5661
X-RAY DIFFRACTION	r_scbond_it	2.81	3.238	4299
X-RAY DIFFRACTION	r_scbond_other	2.81	3.239	4300
X-RAY DIFFRACTION	r_scangle_it	4.588	5.773	6315
X-RAY DIFFRACTION	r_scangle_other	4.588	5.774	6316
X-RAY DIFFRACTION	r_lrange_it	6.67	30.463	9782
X-RAY DIFFRACTION	r_lrange_other	6.646	30.022	9750
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.027	0.05	6816
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.042	0.05	6613
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.051	0.05	4041

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.02686	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.02686	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.04171	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.04171	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.05086	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.05086	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.56-2.626	0.451	175	0.394	3647	0.396	3851	0.867	0.903	99.2469	0.399
2.626-2.698	0.374	141	0.402	3573	0.401	3746	0.916	0.893	99.1458	0.406
2.698-2.776	0.406	137	0.374	3465	0.375	3625	0.892	0.909	99.3655	0.371
2.776-2.861	0.318	140	0.328	3399	0.328	3544	0.934	0.933	99.8589	0.321
2.861-2.955	0.327	138	0.301	3310	0.302	3457	0.931	0.943	99.7397	0.289
2.955-3.058	0.295	133	0.262	3177	0.264	3318	0.943	0.956	99.7589	0.247
3.058-3.173	0.235	137	0.244	3075	0.244	3222	0.964	0.963	99.6896	0.222
3.173-3.302	0.249	124	0.234	2933	0.235	3061	0.959	0.968	99.8693	0.214
3.302-3.448	0.238	102	0.226	2828	0.226	2949	0.97	0.974	99.3557	0.208
3.448-3.616	0.222	124	0.205	2730	0.206	2857	0.97	0.979	99.895	0.19
3.616-3.81	0.249	100	0.197	2594	0.199	2718	0.96	0.98	99.117	0.182
3.81-4.04	0.211	103	0.181	2426	0.183	2556	0.975	0.982	98.9437	0.164
4.04-4.316	0.198	86	0.149	2298	0.15	2389	0.979	0.988	99.7907	0.136
4.316-4.659	0.177	93	0.135	2161	0.136	2260	0.983	0.989	99.7345	0.125
4.659-5.099	0.174	84	0.137	1998	0.138	2089	0.983	0.99	99.6649	0.126
5.099-5.694	0.182	67	0.139	1792	0.141	1862	0.979	0.99	99.8389	0.129
5.694-6.56	0.179	65	0.158	1608	0.159	1681	0.984	0.988	99.5241	0.145
6.56-7.999	0.218	70	0.175	1354	0.177	1425	0.973	0.983	99.9298	0.162
7.999-11.166	0.155	39	0.143	1065	0.143	1110	0.98	0.988	99.4595	0.145
11.166-49.21	0.197	28	0.204	638	0.203	669	0.98	0.975	99.5516	0.215

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	0.972	-0.0941	-0.534	0.4017	0.0407	1.9617	-0.0063	0.0973	-0.0354	-0.0472	0.0173	-0.0725	0.0211	0.0513	-0.011	0.103	-0.0168	-0.0246	0.0208	-0.0173	0.234	17.6407	-8.1989	49.7537
2	0.9817	-0.0678	0.4699	0.4342	-0.0741	1.9425	-0.0298	0.1251	0.0524	-0.0755	0.0131	0.0664	-0.0767	-0.0236	0.0167	0.0992	-0.0243	0.0029	0.0273	0.0243	0.2394	-0.8849	63.7661	49.6351
3	0.6695	0.1124	-0.358	0.8005	0.2687	1.3757	0.0215	0.2377	0.0693	-0.2476	0.0621	-0.0094	-0.1567	0.0096	-0.0836	0.1482	-0.0056	-0.0241	0.1204	0.0448	0.2728	23.3057	7.5298	42.7331
4	0.7216	0.1522	0.4598	0.8253	-0.3324	1.7333	0.0287	0.2438	-0.0781	-0.2146	0.0787	0.0469	0.1725	-0.0197	-0.1074	0.1245	-0.0128	0.0012	0.1396	-0.0449	0.267	-6.4741	48.0463	42.565
5	1.7968	-1.284	-0.068	3.9159	0.2199	1.6476	-0.0151	-0.1904	0.0502	0.2873	0.0754	0.0418	0.0279	-0.113	-0.0604	0.1354	-0.0125	-0.0393	0.1465	-0.0113	0.1835	8.6746	7.3384	88.6407
6	1.5133	-0.2443	0.1113	2.4248	-0.2316	1.8944	0.0079	-0.0882	-0.0069	0.3139	0.0131	0.0222	-0.0694	0.0378	-0.0209	0.153	-0.0111	0.0192	0.1139	0	0.1828	8.6795	47.9998	88.5453

Refinement TLS group

Selection: ALL

-
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

-
Protein , 1 types, 2 molecules EF

-
Antibody , 2 types, 4 molecules ABCD

-
Non-polymers , 3 types, 402 molecules

-
Details

-
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

-Protein , 1 types, 2 molecules EF

-Antibody , 2 types, 4 molecules ABCD

-Non-polymers , 3 types, 402 molecules

-Details

-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

-
Protein , 1 types, 2 molecules EF

-
Antibody , 2 types, 4 molecules ABCD

-
Non-polymers , 3 types, 402 molecules

-
Details

-
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