PDB-9cds: Crystal structure of OspA ST1 from B. burgdorferi bound to monocl...

ID or keywords:

Entry

Database: PDB / ID: 9cds

Title

Crystal structure of OspA ST1 from B. burgdorferi bound to monoclonal antibody LA-2

Components

Hybridoma Antibody LA2 (Heavy Chain)
Hybridoma Antibody LA2 (Light Chain)
Outer surface protein A

Keywords

IMMUNE SYSTEM / Lyme disease / Outer Surface Protein A (OspA)

Function / homology

Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / cell surface / membrane / Outer surface protein A

Function and homology information

Biological species

Mus musculus (house mouse)

Borreliella burgdorferi B31 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Laciak, A.R. / Lai, Y.-T. / Dhingra, Y.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Preclinical assessment of an investigational mRNA lipid nanoparticle OspA vaccine for Lyme disease
Authors: Finn, M.B. / Dold, C. / Willsey, G. / Piazza, C.L. / Clendenen, L. / Shrestha, M. / You, S.S. / Ma, L. / Dhingra, Y. / Laciak, A.R. / Uggowitzer, K.A. / Obiero, J.M. / Natarajan, H. / Green, ...

History

Deposition	Jun 25, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 24, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9cds.cif.gz	677 KB	Display	PDBx/mmCIF format
PDB format	pdb9cds.ent.gz	426.3 KB	Display	PDB format
PDBx/mmJSON format	9cds.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9cds_validation.pdf.gz	459.1 KB	Display	wwPDB validaton report
Full document	9cds_full_validation.pdf.gz	468 KB	Display
Data in XML	9cds_validation.xml.gz	57.9 KB	Display
Data in CIF	9cds_validation.cif.gz	78.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cd/9cds ftp://data.pdbj.org/pub/pdb/validation_reports/cd/9cds	HTTPS FTP

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Related structure data

Similar structure data	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
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

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)
#261 - Sep 2021
DNA-Sequencing Nanopores
similarity (1)
#22 - Oct 2001
Photosystem I
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#29 - May 2002
Penicillin-binding Proteins
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: Hybridoma Antibody LA2 (Light Chain)

B: Hybridoma Antibody LA2 (Heavy Chain)

C: Outer surface protein A

D: Hybridoma Antibody LA2 (Light Chain)

E: Hybridoma Antibody LA2 (Heavy Chain)

F: Outer surface protein A

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	68.555, 68.555, 619.736
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

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:

Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	ASP	ASP	ASN	ASN	1 - 210	1 - 210
2	1	1	ASP	ASP	ASN	ASN	1 - 210	1 - 210
3	2	2	ASP	ASP	GLU	GLU	1 - 213	1 - 213
4	2	2	ASP	ASP	GLU	GLU	1 - 213	1 - 213
5	3	3	SER	SER	THR	THR	26 - 200	26 - 200
6	3	3	SER	SER	THR	THR	26 - 200	26 - 200

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

#1: Antibody	Hybridoma Antibody LA2 (Light Chain) Mass: 23608.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody	Hybridoma Antibody LA2 (Heavy Chain) Mass: 22629.268 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein	Outer surface protein A Mass: 31632.783 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: ospA, BB_A15 / Production host: Homo sapiens (human) / References: UniProt: P0CL66
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 563 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 54.43 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 15 mg/mL, 0.1 M Magnesium Acetate tetrahydrate and 10% (w/v) PEG 3350; cryo 25%(v/v) Glycerol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08ID-1 / Wavelength: 0.9537 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 26, 2023

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9537 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.4951
pseudo-merohedral	2	2	-K, -H, -L	2	0.5049

Reflection

Resolution: 1.85→68.86 Å / Num. obs: 139556 / % possible obs: 100 % / Redundancy: 19.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.125 / R_pim(I) all: 0.029 / R_rim(I) all: 0.129 / Χ²: 1.03 / Net I/σ(I): 17

Reflection shell

Resolution: 1.85→1.88 Å / Redundancy: 18.8 % / R_merge(I) obs: 2.821 / Mean I/σ(I) obs: 1 / Num. unique obs: 6793 / CC_1/2: 0.304 / R_pim(I) all: 0.661 / R_rim(I) all: 2.889 / Χ²: 0.66 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.85→59.1 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.947 / SU B: 3.787 / SU ML: 0.07 / Cross valid method: FREE R-VALUE / ESU R: 0.028 / ESU R Free: 0.027
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2333	6937	4.981 %	Random
R_work	0.2023	132341	-	-
all	0.204	-	-	-
obs	-	139278	99.985 %	-

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: 40.945 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.614 Å²	0 Å²	-0 Å²
2-	-	-2.614 Å²	-0 Å²
3-	-	-	5.227 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→59.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10205	0	0	563	10768

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	10439
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	9827
X-RAY DIFFRACTION	r_angle_refined_deg	1.282	1.825	14148
X-RAY DIFFRACTION	r_angle_other_deg	0.452	1.77	22889
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.087	5	1355
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	20.678	5	28
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.778	10	1886
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.06	10	389
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	1646
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	11929
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2115
X-RAY DIFFRACTION	r_nbd_refined	0.192	0.2	1705
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.205	0.2	9056
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	4955
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	5561
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.182	0.2	570
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.062	0.2	9
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.073	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.142	0.2	40
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.184	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	1.604	3.042	5378
X-RAY DIFFRACTION	r_mcbond_other	1.604	3.042	5378
X-RAY DIFFRACTION	r_mcangle_it	2.251	5.466	6714
X-RAY DIFFRACTION	r_mcangle_other	2.251	5.466	6715
X-RAY DIFFRACTION	r_scbond_it	1.592	3.099	5061
X-RAY DIFFRACTION	r_scbond_other	1.592	3.099	5062
X-RAY DIFFRACTION	r_scangle_it	2.209	5.683	7423
X-RAY DIFFRACTION	r_scangle_other	2.209	5.683	7424
X-RAY DIFFRACTION	r_lrange_it	3.895	36.59	42881
X-RAY DIFFRACTION	r_lrange_other	3.885	36.563	42611
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.136	0.05	6361
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.149	0.05	5779
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.175	0.05	6801

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	0.13607	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.13607	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.14921	0.05007
2	4	A	X-RAY DIFFRACTION	Local ncs	0.14921	0.05007
3	5	A	X-RAY DIFFRACTION	Local ncs	0.17496	0.05007
3	6	A	X-RAY DIFFRACTION	Local ncs	0.17496	0.05007

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 (%)
1.85-1.898	0.661	493	0.572	9713	X-RAY DIFFRACTION	99.863
1.898-1.95	0.464	526	0.422	9573	X-RAY DIFFRACTION	100
1.95-2.006	0.377	526	0.321	9199	X-RAY DIFFRACTION	100
2.006-2.068	0.303	454	0.256	9006	X-RAY DIFFRACTION	100
2.068-2.136	0.262	460	0.214	8762	X-RAY DIFFRACTION	100
2.136-2.211	0.256	458	0.211	8485	X-RAY DIFFRACTION	100
2.211-2.294	0.259	417	0.203	8128	X-RAY DIFFRACTION	100
2.294-2.388	0.245	380	0.197	7834	X-RAY DIFFRACTION	100
2.388-2.494	0.251	355	0.207	7544	X-RAY DIFFRACTION	100
2.494-2.615	0.225	342	0.193	7234	X-RAY DIFFRACTION	100
2.615-2.757	0.237	347	0.195	6897	X-RAY DIFFRACTION	100
2.757-2.923	0.241	385	0.195	6370	X-RAY DIFFRACTION	100
2.923-3.125	0.241	324	0.195	6174	X-RAY DIFFRACTION	100
3.125-3.375	0.204	283	0.2	5592	X-RAY DIFFRACTION	100
3.375-3.696	0.228	297	0.198	5220	X-RAY DIFFRACTION	99.9819
3.696-4.131	0.196	237	0.175	4712	X-RAY DIFFRACTION	100
4.131-4.767	0.164	253	0.151	4128	X-RAY DIFFRACTION	100
4.767-5.831	0.204	195	0.172	3506	X-RAY DIFFRACTION	100
5.831-8.217	0.236	119	0.201	2744	X-RAY DIFFRACTION	99.9302
8.217-59.1	0.182	86	0.17	1520	X-RAY DIFFRACTION	99.7515

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	0.7009	-0.297	-0.5488	0.3391	0.4392	0.8604	-0.0655	-0.0912	-0.0349	0.1287	0.01	0.0782	0.1208	-0.0485	0.0555	0.0707	0.0284	0.0426	0.09	0.0183	0.0275	-49.7402	26.446	15.5462
2	1.1305	-0.0303	-0.8297	0.0451	0.0134	0.9213	0.0334	-0.143	-0.0035	0.0458	-0.0105	0.0318	-0.0406	-0.0233	-0.0229	0.1019	0.0195	0.0084	0.1293	-0.0135	0.0376	-35.0896	34.2074	21.9851
3	0.4262	-0.2399	-0.8066	0.1877	0.4977	1.722	0.0037	-0.0133	-0.0246	-0.1025	0.0632	-0.0175	0.0106	0.2324	-0.0669	0.2747	0.0342	0.0361	0.3005	-0.0548	0.1211	-14.0605	15.081	-38.0263
4	0.7547	-0.396	-0.6994	0.3839	0.3936	1.1354	-0.023	0.1251	-0.0922	-0.0612	-0.0255	-0.0083	0.0945	-0.0518	0.0486	0.0558	0.0145	0.0264	0.0992	-0.0191	0.0336	-55.013	29.3966	-7.4706
5	0.4198	-0.6471	-0.5654	1.1926	0.8769	1.0978	0.0551	0.0569	-0.0108	-0.1692	-0.0276	-0.0151	-0.051	0.0234	-0.0275	0.0885	0.0207	0.0218	0.1359	0.0228	0.0375	-55.4041	45.6033	-14.2968
6	0.2862	-0.0923	-0.6178	0.0764	0.2312	1.4959	0.0578	-0.0663	0.0068	0.0634	-0.0246	0.0366	-0.1425	-0.0639	-0.0333	0.2168	0.0089	0.0607	0.2859	0.0006	0.0945	-82.3003	54.9402	45.7855

Refinement TLS group

Selection: ALL

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