PDB-8t58: Structure of VHH-Fab complex with engineered FNQIKG elbow region

ID or keywords:

Entry

Database: PDB / ID: 8t58

Title

Structure of VHH-Fab complex with engineered FNQIKG elbow region

Components

Fab heavy chain
Fab light chain
VHH domain

Keywords

IMMUNE SYSTEM / NabFab / Nanobody / Antibody Fragment

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.23 Å

Authors

Filippova, E.V. / Kossiakoff, A.A.

Funding support

United States, 1items

Citation

Journal: Protein Sci. / Year: 2024
Title: Engineered antigen-binding fragments for enhanced crystallization of antibody:antigen complexes.
Authors: Bruce, H.A. / Singer, A.U. / Filippova, E.V. / Blazer, L.L. / Adams, J.J. / Enderle, L. / Ben-David, M. / Radley, E.H. / Mao, D.Y.L. / Pau, V. / Orlicky, S. / Sicheri, F. / Kurinov, I. / ...

History

Deposition	Jun 12, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 29, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jan 3, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.name
Revision 1.2	Nov 20, 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	8t58.cif.gz	451.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8t58.ent.gz	367.8 KB	Display	PDB format
PDBx/mmJSON format	8t58.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8t58_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	8t58_full_validation.pdf.gz	1.7 MB	Display
Data in XML	8t58_validation.xml.gz	45.1 KB	Display
Data in CIF	8t58_validation.cif.gz	65.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t5/8t58 ftp://data.pdbj.org/pub/pdb/validation_reports/t5/8t58	HTTPS FTP

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Related structure data

Related structure data	8t6iC 8t7fC 8t7gC 8t7iC 8t8iC 8t9yC 8trsC 8trtC 8ts5C C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: VHH domain

B: Fab light chain

C: Fab heavy chain

D: VHH domain

E: Fab light chain

F: Fab heavy chain

hetero molecules

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

1

A: VHH domain

B: Fab light chain

C: Fab heavy chain

hetero molecules

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

2

D: VHH domain

E: Fab light chain

F: Fab heavy chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	65.771, 119.826, 82.244
Angle α, β, γ (deg.)	90.00, 93.35, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Antibody , 3 types, 6 molecules ADBECF

#1: Antibody	VHH domain Mass: 14170.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET26B+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Antibody	Fab light chain Mass: 23258.783 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PRH2.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#3: Antibody	Fab heavy chain Mass: 25753.609 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: RH2.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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Non-polymers , 3 types, 572 molecules

#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 568 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
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: 2.56 Å³/Da / Density % sol: 51.96 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 4% Tacsimate, 12% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 24, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.23→119.83 Å / Num. obs: 61587 / % possible obs: 99.1 % / Redundancy: 6.9 % / CC_1/2: 0.99 / R_pim(I) all: 0.03 / Net I/σ(I): 16.1
Reflection shell	Resolution: 2.23→2.29 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4313 / CC_1/2: 0.86 / R_pim(I) all: 0.24

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.23→67.73 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.945 / SU B: 12.632 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2252	2955	4.8 %	RANDOM
R_work	0.18246	-	-	-
obs	0.18451	58606	99.04 %	-

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: 49.915 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.87 Å²	-0 Å²	-1.76 Å²
2-	-	-0.72 Å²	0 Å²
3-	-	-	-0.94 Å²

Refinement step

Cycle: 1 / Resolution: 2.23→67.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8600	0	14	569	9183

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	8809
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.035	1.635	11925
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.561	5	1087
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.739	22.398	392
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.207	15	1388
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.433	15	39
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	1146
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	6610
X-RAY DIFFRACTION	r_gen_planes_other
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	1.34	3.523	4465
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.338	5.268	5513
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.427	3.619	4344
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined	5.605	47.265	13108
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

LS refinement shell

Resolution: 2.23→2.285 Å

	R_factor	Num. reflection	% reflection
R_free	0.266	203	-
R_work	0.24	4102	-
obs	-	-	93.57 %

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	2.2432	2.9944	-2.0667	6.7917	-2.591	2.5876	0.0861	0.1897	0.1495	0.2668	-0.0859	0.1465	-0.2178	-0.3164	-0.0002	0.0439	0.0166	-0.0273	0.1769	0.0487	0.0712	10.7913	10.5074	-49.7166
2	1.552	1.188	-0.4841	5.1822	-1.8345	4.149	-0.2605	0.2809	-0.0275	-0.1912	-0.1623	-0.646	0.0301	-0.0017	0.4228	0.0509	-0.0245	0.0119	0.1776	0.0755	0.1255	18.7506	6.9624	-50.6237
3	1.8925	3.0776	0.1316	11.993	0.8598	3.2166	-0.0736	0.0978	0.2004	-0.1967	-0.154	0.1729	-0.1772	-0.1204	0.2275	0.0613	0.0223	-0.0117	0.0979	0.0286	0.0456	12.1794	6.952	-42.12
4	2.5153	-0.12	-0.6046	5.0564	1.7038	1.3663	-0.0759	-0.0538	-0.0059	0.1305	-0.0352	-0.0438	0.3516	0.0048	0.1111	0.1399	-0.0222	0.0552	0.0898	-0.005	0.024	4.0577	-16.2073	-18.8158
5	0.5367	0.069	-0.3257	0.5179	-0.5096	2.2029	-0.1002	0.0384	-0.0214	-0.0386	-0.0035	-0.0902	0.2668	0.1061	0.1038	0.0638	0.0201	0.0405	0.0912	-0.0179	0.0756	9.5452	-14.0543	-14.811
6	1.6112	0.4845	-0.4034	1.3706	0.8506	3.3313	-0.0358	-0.1583	-0.1634	0.1739	-0.0301	-0.0409	0.428	0.1181	0.0659	0.1448	0.068	0.0311	0.0623	0.0394	0.029	4.6916	-22.543	9.845
7	1.6108	-0.1449	0.6969	2.0759	0.5758	3.0431	0.0028	0.0112	0.2316	0.1219	-0.0862	-0.1253	-0.4545	0.2605	0.0833	0.1121	-0.0334	0.0002	0.1326	0.0133	0.0668	18.2457	7.5696	-18.388
8	1.4088	-0.1527	0.2748	0.6831	0.0725	3.1721	-0.0175	-0.0073	0.2107	0.021	-0.0071	0.0089	-0.3601	-0.0217	0.0246	0.0918	0.0097	0.0235	0.0793	0.0064	0.0659	13.2578	8.4538	-20.7649
9	1.2396	0.3515	-0.8915	2.6306	-1.4364	4.0633	0.0539	-0.1329	-0.0611	0.2377	-0.1205	0.0281	-0.1537	0.5745	0.0667	0.0401	0.0245	-0.0126	0.177	-0.0085	0.0267	18.5698	-7.4989	6.953
10	1.7311	-0.7033	0.0567	4.7683	-0.3201	1.3551	-0.0883	-0.1862	-0.2302	0.0978	0.1341	-0.3673	0.104	0.4719	-0.0458	0.0524	0.0871	0.01	0.2306	0.0039	0.0843	21.8517	-16.0251	8.5163
11	4.0105	-1.7373	-0.0202	7.1149	-0.3726	2.213	-0.1078	-0.1574	0.4963	0.3148	-0.0945	-0.5086	-0.2423	0.1516	0.2023	0.0378	-0.0129	-0.0465	0.2462	-0.074	0.1151	-12.3757	13.0193	36.7805
12	4.1376	-0.8648	-0.7214	3.9564	-0.5465	4.2519	0.0003	-0.5266	0.3028	0.2699	0.0742	0.6104	-0.3415	-0.3942	-0.0744	0.0406	0.0326	0.0408	0.293	-0.0962	0.154	-22.0361	12.732	39.5233
13	4.3286	2.0624	-1.7488	4.5698	-0.2512	4.3745	0.0643	-0.016	0.7706	-0.4101	0.4654	0.6772	-0.0633	-0.6013	-0.5298	0.0661	-0.0239	-0.0398	0.3567	0.0695	0.231	-23.2351	13.2226	32.5399
14	3.1319	-0.2201	-0.5135	5.3243	-0.564	0.9749	0.0161	-0.0701	0.0342	0.298	-0.0098	-0.0083	0.2814	0.1008	-0.0064	0.1459	0.0262	0.0082	0.0963	-0.0043	0.0131	-9.2127	-14.7372	9.8335
15	8.3252	3.6875	-3.5972	7.2769	-5.7808	4.6849	0.8666	0.4198	0.0691	0.0194	-1.0991	-0.4341	-0.2134	0.8272	0.2325	0.7535	-0.2865	0.3245	0.6198	0.0124	0.368	-1.1176	1.1517	14.4805
16	0.4717	-0.0374	-0.0495	0.8732	1.0435	1.473	-0.0754	-0.0443	-0.0424	0.0715	-0.0224	0.0179	0.2207	-0.0764	0.0978	0.0991	-0.0196	0.0484	0.105	0.0115	0.0583	-13.6261	-15.0259	0.2431
17	1.2968	-0.5845	1.3602	2.3255	-2.002	7.3523	-0.0017	0.1981	-0.1431	-0.2146	-0.0165	-0.0039	0.2177	0.164	0.0182	0.0748	-0.0339	0.0522	0.0583	-0.0521	0.0602	-9.4992	-26.9808	-24.3073
18	1.1781	0.0951	0.796	1.9464	-0.4441	2.3694	0.0202	-0.1273	0.2093	-0.1176	-0.0942	0.1536	-0.2875	-0.2976	0.074	0.0743	0.0353	0.0026	0.1622	-0.0493	0.1238	-24.0554	8.7966	7.7482
19	2.4001	-0.2649	-1.7765	1.8073	2.3672	5.7349	-0.0233	0.0701	0.2779	-0.2454	-0.019	-0.0343	-0.5711	-0.1629	0.0423	0.1225	0.0286	0.0102	0.0109	0.0096	0.1362	-20.3495	15.2781	3.1933
20	0.4673	0.2103	0.1726	0.8451	0.9895	2.0236	-0.0436	-0.0355	0.0333	-0.0574	-0.0147	-0.0431	-0.0612	-0.046	0.0584	0.0546	-0.0033	0.0359	0.1031	0.0003	0.0828	-19.8133	-1.734	0.7921
21	0.5925	0.2649	0.3525	4.8429	0.5381	1.0922	-0.0927	-0.0064	-0.0127	-0.0905	0.0634	0.3142	-0.0197	-0.2155	0.0293	0.0585	-0.0324	0.036	0.0846	-0.0142	0.0557	-27.235	-16.4723	-17.3528

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 34
2	X-RAY DIFFRACTION	2	A	35 - 122
3	X-RAY DIFFRACTION	3	A	125 - 137
4	X-RAY DIFFRACTION	4	B	4 - 23
5	X-RAY DIFFRACTION	5	B	32 - 159
6	X-RAY DIFFRACTION	6	B	160 - 231
7	X-RAY DIFFRACTION	7	C	1 - 62
8	X-RAY DIFFRACTION	8	C	63 - 128
9	X-RAY DIFFRACTION	9	C	129 - 152
10	X-RAY DIFFRACTION	10	C	157 - 240
11	X-RAY DIFFRACTION	11	D	3 - 31
12	X-RAY DIFFRACTION	12	D	32 - 113
13	X-RAY DIFFRACTION	13	D	114 - 137
14	X-RAY DIFFRACTION	14	E	4 - 23
15	X-RAY DIFFRACTION	15	E	24 - 31
16	X-RAY DIFFRACTION	16	E	32 - 200
17	X-RAY DIFFRACTION	17	E	201 - 232
18	X-RAY DIFFRACTION	18	F	-2 - 62
19	X-RAY DIFFRACTION	19	F	63 - 94
20	X-RAY DIFFRACTION	20	F	95 - 158
21	X-RAY DIFFRACTION	21	F	159 - 240

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