PDB-9bx5: Human Fab 8C1 in complex with OspCA peptide P4 (residues 141-144)

ID or keywords:

Entry

Database: PDB / ID: 9bx5

Title

Human Fab 8C1 in complex with OspCA peptide P4 (residues 141-144)

Components

8C1 Fab Heavy Chain
8C1 Fab Light Chain
P4 peptide from Outer surface protein C

Keywords

IMMUNE SYSTEM / Human Fab / Peptide of Outer Surface Protein C type A (OspCA)

Function / homology

external side of cell outer membrane / Lipoprotein, OspC-type / Outer surface protein C-like superfamily / Lipoprotein / Prokaryotic membrane lipoprotein lipid attachment site profile. / cell surface / membrane / Outer surface protein C

Function and homology information

Biological species

Homo sapiens (human)

Borreliella burgdorferi (Lyme disease spirochete)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.57 Å

Authors

Rudolph, M.J. / Mantis, N.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Human Fab 8C1 in complex with OspCA peptide P4 (residues 141-144)
Authors: Rudolph, M.J. / Mantis, N.

History

Deposition	May 22, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 27, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9bx5.cif.gz	323.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9bx5.ent.gz	219.1 KB	Display	PDB format
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Others	Other downloads

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Validation report

Summary document	9bx5_validation.pdf.gz	444 KB	Display	wwPDB validaton report
Full document	9bx5_full_validation.pdf.gz	446 KB	Display
Data in XML	9bx5_validation.xml.gz	29.5 KB	Display
Data in CIF	9bx5_validation.cif.gz	43.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bx/9bx5 ftp://data.pdbj.org/pub/pdb/validation_reports/bx/9bx5	HTTPS FTP

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Related structure data

Related structure data	9b88
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

H: 8C1 Fab Heavy Chain

L: 8C1 Fab Light Chain

P: P4 peptide from Outer surface protein C

hetero molecules

48.3 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)	67.657, 69.389, 95.102
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁22₁
Space group name Hall	P22ab(y,z,x)
Symmetry operation	#1: x,y,z #2: x+1/2,-y,-z+1/2 #3: -x,y,-z #4: -x+1/2,-y,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	H-691- HOH

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide	P4 peptide from Outer surface protein C / pC / P23 Mass: 501.533 Da / Num. of mol.: 1 / Fragment: residues 141-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete) Strain: B31 / Gene: ospC, BB_B19 / Production host: Escherichia coli B (bacteria) / References: UniProt: Q07337

#3: Protein/peptide

P4 peptide from Outer surface protein C / pC / P23

Mass: 501.533 Da / Num. of mol.: 1 / Fragment: residues 141-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Borreliella burgdorferi (Lyme disease spirochete)
Strain: B31 / Gene: ospC, BB_B19 / Production host:

Escherichia coli B (bacteria) / References: UniProt: Q07337

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Antibody , 2 types, 2 molecules HL

#1: Antibody	8C1 Fab Heavy Chain Mass: 23659.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody	8C1 Fab Light Chain Mass: 23965.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 3 types, 698 molecules

#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 693 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 2.39 Å³/Da / Density % sol: 48.61 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 200 mM sodium nitrate and 20% PEG 3,350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.979 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 12, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.57→50 Å / Num. obs: 63082 / % possible obs: 99.8 % / Redundancy: 12.3 % / B_iso Wilson estimate: 13.52 Å² / CC_1/2: 0.999 / Net I/σ(I): 51
Reflection shell	Resolution: 1.57→1.6 Å / Num. unique obs: 3046 / CC_1/2: 0.994

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.57→38.9 Å / SU ML: 0.1115 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 15.132
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1697	3082	4.9 %
R_work	0.1416	59804	-
obs	0.143	62886	99.58 %

Solvent computation

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

Displacement parameters

B_iso mean: 20.26 Å²

Refinement step

Cycle: LAST / Resolution: 1.57→38.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3277	0	8	693	3978

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0081	3411
X-RAY DIFFRACTION	f_angle_d	1.0736	4646
X-RAY DIFFRACTION	f_chiral_restr	0.0626	530
X-RAY DIFFRACTION	f_plane_restr	0.0091	594
X-RAY DIFFRACTION	f_dihedral_angle_d	6.7641	473

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 (%)
1.57-1.59	0.1942	135	0.161	2505	X-RAY DIFFRACTION	93.88
1.59-1.62	0.1934	117	0.1534	2698	X-RAY DIFFRACTION	98.6
1.62-1.65	0.197	155	0.1559	2674	X-RAY DIFFRACTION	99.79
1.65-1.68	0.1993	113	0.1514	2696	X-RAY DIFFRACTION	99.89
1.68-1.71	0.1925	139	0.1482	2683	X-RAY DIFFRACTION	99.96
1.71-1.75	0.2364	131	0.1469	2705	X-RAY DIFFRACTION	100
1.75-1.78	0.1602	136	0.1419	2732	X-RAY DIFFRACTION	99.97
1.78-1.83	0.1608	148	0.1422	2701	X-RAY DIFFRACTION	100
1.83-1.87	0.1776	133	0.1396	2687	X-RAY DIFFRACTION	99.96
1.87-1.92	0.1806	156	0.1412	2691	X-RAY DIFFRACTION	99.93
1.92-1.98	0.167	130	0.1421	2724	X-RAY DIFFRACTION	100
1.98-2.04	0.1682	152	0.1402	2694	X-RAY DIFFRACTION	99.93
2.04-2.12	0.172	129	0.1358	2741	X-RAY DIFFRACTION	99.97
2.12-2.2	0.1482	144	0.1286	2703	X-RAY DIFFRACTION	100
2.2-2.3	0.1748	151	0.132	2724	X-RAY DIFFRACTION	100
2.3-2.42	0.1696	144	0.133	2725	X-RAY DIFFRACTION	99.97
2.42-2.57	0.1503	149	0.14	2726	X-RAY DIFFRACTION	100
2.57-2.77	0.1727	123	0.1492	2760	X-RAY DIFFRACTION	99.86
2.77-3.05	0.1717	138	0.1501	2756	X-RAY DIFFRACTION	99.9
3.05-3.49	0.1789	148	0.1404	2768	X-RAY DIFFRACTION	99.9
3.49-4.4	0.1608	162	0.1314	2786	X-RAY DIFFRACTION	99.86
4.4-38.9	0.1576	149	0.1506	2925	X-RAY DIFFRACTION	99.39

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	1.15032229742	-0.681182469443	0.733400269494	6.6216296959	-4.58625292956	3.79918742734	-0.0143177120495	-0.0892081314762	0.180812040255	-0.0154746425517	0.0345937264786	0.264248814594	-0.033202393752	-0.0899521414981	-0.00455681016091	0.127823235859	0.0136454360832	-0.039019947294	0.0808458142086	-0.0196782504139	0.0901660212739	13.1393657452	63.5428888891	35.3370081886
2	2.48654394772	-2.17971170034	0.349200955084	6.54433936618	-1.61490779255	1.11423825485	0.107921594392	0.0898646030748	0.0923648444182	-0.0364735546401	-0.0881253270671	0.209861007614	-0.126327624485	-0.27557216061	-0.0427354944014	0.155558603159	0.0541877241707	-0.0327032247051	0.134123334879	0.0215728845366	0.182869744986	7.60924418742	69.0387247499	29.1311638994
3	1.60702760014	0.157801214783	-0.296955078043	6.85018977617	-3.2853766505	3.21508674623	0.0476114704894	0.0883552882611	0.230419252142	-0.262553915628	-0.229756587265	-0.223747347796	0.056919142292	0.0140469223406	0.207243848865	0.111901266969	0.0201669502842	-0.0387295211802	0.118347276071	0.0371051392478	0.156248361418	16.3848786295	63.6022596428	30.5637131289
4	2.35817352094	-0.506672898077	0.146145591936	5.14999050151	-1.42512313599	2.94732161553	-0.0447572606951	-0.230110211969	0.419329324778	0.685269816711	0.139175326043	0.256186947692	-0.563666919771	-0.211148542973	-0.0980674839101	0.212002986331	0.0366580302999	-0.0312944231768	0.118220594763	-0.0337699826995	0.187704592665	12.2510421913	71.9880984005	38.8464292514
5	5.05790660775	-6.23799102929	-4.25493916917	9.77285511185	2.63643441342	6.91758458871	-0.300462536964	-0.266378408541	-0.732802171758	0.0986953071679	0.216855157085	0.500685601032	0.28660500739	0.0413633081865	0.0920309147928	0.166244263452	-0.0303299876007	0.0379711931042	0.126576557959	0.0151391567847	0.182496382379	-0.43354235174	22.2792503729	17.0580288392
6	2.1367536444	0.0816551202253	0.191172901882	6.2351709091	-1.26928213885	1.24192455202	-0.24478263603	0.307648163987	0.179957943478	-0.383175607454	0.185980400648	-0.421706169427	-0.0245078264631	0.0877512916073	0.262242490877	0.102785837588	-0.0466641486977	-0.0125294845544	0.192297774959	0.0442177501387	0.0714155385878	14.4759352657	39.8605146883	8.9595965793
7	2.25770314672	1.50750148224	-0.214214318365	5.0424812205	-2.19087862407	2.40655216232	-0.219346391229	0.5729639005	-0.283941269369	-0.144315961205	0.215436028712	-0.273257631705	0.0461947595858	0.145451653892	0.080210437593	0.101996093539	-0.030468156807	0.0239051393726	0.208308362579	-0.041391102418	0.0767280209694	11.1402914711	27.3483186134	8.29789935371
8	2.74179259402	0.540769104822	-0.0147849413405	3.85088317183	0.281135438598	1.85034761839	-0.120595216277	0.267292159825	0.141014003238	-0.0570656371151	0.0804160469317	0.212057918647	-0.107933645232	-0.0396223333151	0.0512481671612	0.0502786943193	-0.00426854009054	-0.0121767884356	0.109403276268	0.0518328724741	0.0536023903712	2.78150170678	34.9567217112	13.3099182672
9	2.63315253813	0.269807361158	-0.137581508887	2.01731175358	0.221349121782	0.685329345383	-0.346226030717	0.991561057053	-0.0231945615681	-0.962565696198	0.29202207605	0.330120114834	-0.128042067862	-0.130019952516	-0.0249793457663	-0.00188779183834	-0.0157552021749	-0.168761710958	0.298916073945	0.158657801272	0.123448114014	1.05472384087	35.3616903478	5.80700886975
10	0.978621067958	-0.209663145331	0.669000919467	5.84852799865	-0.4636567936	1.30102780738	-0.336540935064	0.588017717279	0.286535721436	-0.49494552841	0.395759118501	0.196769543294	-0.210716138863	0.122141987259	-0.0420955787643	0.149763528439	-0.0887774371804	-0.0550900141534	0.26893525789	0.130169024574	0.133644773373	6.67303527369	42.6301225043	5.78541979796
11	0.771578732984	0.77895882917	0.125981564194	0.601533286005	0.498428998417	0.566998469738	-0.140760550559	0.286829647461	0.144703451185	-0.107630900841	0.12352854482	0.142236765627	-0.138251118461	0.0399698430756	-0.0482758425636	0.0877278767751	-0.0274977971079	-0.0297925310555	0.106973699049	0.0727509608174	0.0852073566948	11.9724137775	41.4900773849	14.1948100729
12	2.81409475739	0.379307199263	0.948602264039	2.93281147133	0.203924707509	4.09476539013	-0.139624252417	-0.154931717369	0.335026650895	-0.00130694880997	0.0128184484666	0.0442410055183	-0.600393084374	-0.026363155152	0.0917873693754	0.12298601064	-0.00013050936381	-0.0295049635946	0.0657027347938	0.00441821254917	0.147409723208	25.7068055417	66.7754083248	27.8626754372
13	2.03009174413	0.153170039085	-0.115075348697	1.60262878063	0.388575030789	2.50760702116	-0.0787719382775	-0.0154665686459	0.0678610625847	-0.0142265773554	0.0431637931553	0.0308604750585	-0.0825965880088	-0.0378867890582	0.0471021769602	0.107984244733	-0.00444596054573	-0.0253524967422	0.0504532453688	0.0388886173849	0.111333592913	24.8545731377	58.9105798821	26.1060445504
14	4.00122130664	1.71016510458	1.88922707623	3.39590699597	1.9105958714	6.08706855831	-0.0592133870176	-0.0140202938624	0.0625392767443	-0.0768811245572	0.156480903799	-0.244839968032	-0.448973859371	0.439963291394	-0.1203917835	0.122822100405	-0.0440497766104	0.00117170386717	0.106840687776	0.0359222237396	0.139451276463	33.6752054104	63.0832127563	23.549324018
15	2.03084202483	0.600213387283	0.645070428157	1.10667230774	0.223437888431	1.14994728964	0.0335754485928	-0.226416865248	0.0789589902216	0.0730554211575	-0.115681615839	0.0442936148107	-0.00618350212294	-0.0747851016344	0.0704324256415	0.0646683026744	-0.0032213277669	0.0172245953634	0.0881308754306	0.0133800815508	0.0535630784372	-2.66538202165	34.0662220573	32.567900849
16	3.51150045787	1.82690161708	-0.697746255682	2.97871081163	-0.538011098781	1.89492643092	0.0563457225801	-0.147342112297	-0.109813084963	0.0426557367035	-0.0974153793121	-0.219987858339	0.0175064257942	0.156537587355	0.0473502138632	0.0605940568809	0.00649570142446	-0.00814197694213	0.0760322697448	0.0157756764388	0.0576882637606	8.96058170106	33.3224708573	27.5174726683
17	5.89476306653	0.899055313765	1.37946856899	2.94207863975	1.31705008614	4.42653085047	0.223805897213	-0.0165200001419	-0.276168545136	0.143650250995	-0.0482768308048	-0.375605509409	0.338284634955	0.292289729024	-0.21979194608	0.12023695651	0.00885267987749	-0.020428754008	0.0935377960323	0.043101367747	0.136186111579	7.08903360479	23.5731985023	32.3443387425
18	2.54025617224	1.07394798482	0.960200775491	1.23153149028	-0.0696488806099	2.16264756208	0.126223879622	-0.271629085182	-0.164131649083	0.163174761081	-0.127138743152	-0.064056464244	0.0882251965689	0.0768373437847	-0.0110440101204	0.0737421359661	0.00319775957614	0.00495228100002	0.0989418715978	0.0116118182764	0.073362936124	4.5647106439	32.4570800103	35.5864483049
19	1.48063643983	1.76765718797	1.09797851866	2.13788769331	1.13115339677	1.00150756988	0.104886797604	-0.172402965992	0.0628193865855	0.151216563308	-0.148233779818	0.0207302831091	0.0268958056177	-0.10652824202	0.0399760150254	0.0793346685939	-0.00282610352266	0.00700823654921	0.1042515222	-0.00310703560202	0.0926026154365	4.40031546767	41.8871650289	32.4825940504
20	3.02939438142	0.51498596941	-0.835627812595	4.50468066136	-2.07627207595	7.90163982466	0.10967214087	0.100815716036	0.507492706898	-0.102745510922	-0.0698977100937	-0.245498303673	-0.561274400765	0.479143493357	0.0435557570137	0.157063649857	-0.00786979602701	-0.0147292632884	0.0816828459201	0.02647316002	0.217413330904	22.3323805217	73.1420057075	27.507071232

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 'L' and (resid 134 through 155 )	L	B	134 - 155	134 - 155
2	2	chain 'L' and (resid 156 through 168 )	L	B	156 - 168	156 - 168
3	3	chain 'L' and (resid 169 through 193 )	L	B	169 - 193	169 - 193
4	4	chain 'L' and (resid 194 through 216 )	L	B	194 - 216	194 - 216
5	5	chain 'P' and (resid 141 through 144 )	P	C	141 - 144	1 - 4
6	6	chain 'H' and (resid 1 through 17 )	H	A	1 - 17	1 - 17
7	7	chain 'H' and (resid 18 through 32 )	H	A	18 - 32	18 - 32
8	8	chain 'H' and (resid 33 through 57 )	H	A	33 - 57	33 - 57
9	9	chain 'H' and (resid 58 through 76 )	H	A	58 - 76	58 - 76
10	10	chain 'H' and (resid 77 through 91 )	H	A	77 - 91	77 - 91
11	11	chain 'H' and (resid 92 through 120 )	H	A	92 - 120	92 - 120
12	12	chain 'H' and (resid 121 through 146 )	H	A	121 - 146	121 - 142
13	13	chain 'H' and (resid 147 through 189 )	H	A	147 - 189	143 - 185
14	14	chain 'H' and (resid 190 through 214 )	H	A	190 - 214	186 - 210
15	15	chain 'L' and (resid 1 through 37 )	L	B	1 - 37	1 - 37
16	16	chain 'L' and (resid 38 through 53 )	L	B	38 - 53	38 - 53
17	17	chain 'L' and (resid 54 through 66 )	L	B	54 - 66	54 - 66
18	18	chain 'L' and (resid 67 through 95 )	L	B	67 - 95	67 - 95
19	19	chain 'L' and (resid 96 through 118 )	L	B	96 - 118	96 - 118
20	20	chain 'L' and (resid 119 through 133 )	L	B	119 - 133	119 - 133

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