PDB-7wc0: Crystal structure of Fab region of TAU-2212 neutralizing SARS-CoV-2

ID or keywords:

Entry

Database: PDB / ID: 7wc0

Title

Crystal structure of Fab region of TAU-2212 neutralizing SARS-CoV-2

Components

TAU-2212 Heavy chain
TAU-2212 Light chain

Keywords

IMMUNE SYSTEM

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.705 Å

Authors

Xiang, Y. / Li, R. / Ma, B.

Funding support

1items

Citation

Journal: Commun Biol / Year: 2022
Title: Conformational flexibility in neutralization of SARS-CoV-2 by naturally elicited anti-SARS-CoV-2 antibodies.
Authors: Ruofan Li / Michael Mor / Bingting Ma / Alex E Clark / Joel Alter / Michal Werbner / Jamie Casey Lee / Sandra L Leibel / Aaron F Carlin / Moshe Dessau / Meital Gal-Tanamy / Ben A Croker / Ye ...
Abstract: As new variants of SARS-CoV-2 continue to emerge, it is important to assess the cross-neutralizing capabilities of antibodies naturally elicited during wild type SARS-CoV-2 infection. In the present ...

History

Deposition	Dec 17, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 10, 2022	Provider: repository / Type: Initial release
Revision 1.1	Sep 28, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7wc0.cif.gz	319.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7wc0.ent.gz	254 KB	Display	PDB format
PDBx/mmJSON format	7wc0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7wc0_validation.pdf.gz	468.3 KB	Display	wwPDB validaton report
Full document	7wc0_full_validation.pdf.gz	491.5 KB	Display
Data in XML	7wc0_validation.xml.gz	37.1 KB	Display
Data in CIF	7wc0_validation.cif.gz	51.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wc/7wc0 ftp://data.pdbj.org/pub/pdb/validation_reports/wc/7wc0	HTTPS FTP

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Related structure data

Related structure data	32411C 32416C 32417C 32418C 32419C 32420C 32421C 7wbzC 7wcdC 7k8qS S: Starting model for refinement C: citing same article (ref.)

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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)

Deposited unit

H: TAU-2212 Heavy chain

L: TAU-2212 Light chain

A: TAU-2212 Heavy chain

B: TAU-2212 Light chain

104 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

H: TAU-2212 Heavy chain

L: TAU-2212 Light chain

defined by author&software
Evidence: gel filtration
52 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: TAU-2212 Heavy chain

B: TAU-2212 Light chain

defined by author&software
52 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	75.977, 75.977, 348.140
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	170
Space group name H-M	P6₅
Symmetry operation	#1: x,y,z #2: x-y,x,z+5/6 #3: y,-x+y,z+1/6 #4: -y,x-y,z+2/3 #5: -x+y,-x,z+1/3 #6: -x,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	H
2	1	A
3	2	L
4	2	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	VAL	VAL	LYS	LYS	H	A	2 - 222	21 - 241
2	2	1	VAL	VAL	LYS	LYS	A	C	2 - 222	21 - 241
3	3	2	ALA	ALA	HIS	HIS	L	B	3 - 203	22 - 222
4	4	2	ALA	ALA	HIS	HIS	B	D	3 - 203	22 - 222

NCS ensembles :

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

#1: Protein	TAU-2212 Heavy chain Mass: 27087.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody	TAU-2212 Light chain Mass: 24892.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.79 Å³/Da / Density % sol: 55.92 %
Crystal grow	Temperature: 309 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 26% (w/v) polyethylene glycol 3350, 0.2 M (NH4)2SO4, pH 8.0

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL02U1 / Wavelength: 0.98 Å

Detector

Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 26, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.603
1	1	-K, -H, -L	2	0.397

Reflection

Resolution: 2.7→30 Å / Num. obs: 30854 / % possible obs: 100 % / Redundancy: 14.6 % / R_merge(I) obs: 0.137 / R_pim(I) all: 0.037 / R_rim(I) all: 0.142 / Χ²: 1.827 / Net I/σ(I): 7.7 / Num. measured all: 450999

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.7-2.75	14.1	0.904	1532	0.916	0.243	0.937	0.526	100
2.75-2.8	15	0.804	1545	0.926	0.212	0.832	0.556	100
2.8-2.85	15.7	0.723	1517	0.945	0.187	0.747	0.575	100
2.85-2.91	15.8	0.604	1578	0.969	0.156	0.624	0.623	100
2.91-2.97	15.7	0.509	1506	0.975	0.132	0.526	0.658	100
2.97-3.04	15.6	0.455	1559	0.973	0.118	0.47	0.772	100
3.04-3.12	15.2	0.382	1511	0.981	0.101	0.395	0.848	100
3.12-3.2	14.1	0.338	1553	0.981	0.093	0.351	0.923	100
3.2-3.29	14.2	0.268	1569	0.985	0.073	0.278	1.173	100
3.29-3.4	15.1	0.24	1516	0.988	0.064	0.249	1.424	100
3.4-3.52	13.9	0.209	1525	0.986	0.058	0.217	1.779	100
3.52-3.66	14.2	0.183	1542	0.995	0.05	0.19	2.031	100
3.66-3.83	15.2	0.162	1539	0.995	0.044	0.168	2.231	100
3.83-4.03	14.5	0.146	1546	0.993	0.04	0.151	2.633	100
4.03-4.28	13.9	0.115	1542	0.996	0.033	0.119	3.044	99.9
4.28-4.61	13.5	0.098	1531	0.995	0.028	0.102	3.32	100
4.61-5.07	12.9	0.094	1572	0.996	0.028	0.098	3.57	100
5.07-5.8	13.2	0.091	1538	0.998	0.027	0.095	3.542	99.9
5.8-7.3	14.1	0.082	1555	0.997	0.023	0.085	3.386	100
7.3-30	16.5	0.061	1578	0.999	0.015	0.063	3.587	99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-2000	721.4	data scaling
PDB_EXTRACT		data extraction
PHASER		phasing
Coot		model building
HKL-2000		data scaling
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7K8Q

7k8q

Resolution: 2.705→29.746 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.919 / SU B: 21.066 / SU ML: 0.336 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.068
Details: Hydrogens have been used if present in the input file

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2462	1554	5.052 %	RANDOM
R_work	0.2015	29204	-	-
all	0.204	-	-	-
obs	-	30758	99.673 %	-

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: 93.79 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.446 Å²	0 Å²	0 Å²
2-	-	2.446 Å²	0 Å²
3-	-	-	-4.893 Å²

Refinement step

Cycle: LAST / Resolution: 2.705→29.746 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6293	0	0	333	6626

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	6466
X-RAY DIFFRACTION	r_angle_refined_deg	0.969	1.636	8827
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.463	5	829
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.087	23.227	251
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.884	15	977
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.081	15	17
X-RAY DIFFRACTION	r_chiral_restr	0.055	0.2	859
X-RAY DIFFRACTION	r_gen_planes_refined	0.019	0.02	4869
X-RAY DIFFRACTION	r_nbd_refined	0.265	0.2	2841
X-RAY DIFFRACTION	r_nbtor_refined	0.303	0.2	4207
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.249	0.2	348
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.307	0.2	55
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.357	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	4.282	5.445	3337
X-RAY DIFFRACTION	r_mcangle_it	6.379	8.157	4159
X-RAY DIFFRACTION	r_scbond_it	4.084	5.549	3129
X-RAY DIFFRACTION	r_scangle_it	6.027	8.225	4668
X-RAY DIFFRACTION	r_lrange_it	11.351	101.643	25289
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.192	0.05	5240
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.207	0.05	4938

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	H	X-RAY DIFFRACTION	Local ncs	0.19173	0.05007
1	2	A	X-RAY DIFFRACTION	Local ncs	0.19173	0.05007
2	3	L	X-RAY DIFFRACTION	Local ncs	0.2071	0.05007
2	4	B	X-RAY DIFFRACTION	Local ncs	0.2071	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 (%)
2.705-2.775	0.326	112	0.251	2039	X-RAY DIFFRACTION	96.6307
2.775-2.851	0.345	116	0.271	2123	X-RAY DIFFRACTION	100
2.851-2.933	0.296	112	0.265	2086	X-RAY DIFFRACTION	100
2.933-3.024	0.319	100	0.235	1966	X-RAY DIFFRACTION	100
3.024-3.122	0.283	109	0.231	1929	X-RAY DIFFRACTION	100
3.122-3.232	0.351	105	0.243	1854	X-RAY DIFFRACTION	100
3.232-3.354	0.313	103	0.228	1808	X-RAY DIFFRACTION	100
3.354-3.49	0.336	92	0.231	1722	X-RAY DIFFRACTION	100
3.49-3.645	0.225	98	0.211	1679	X-RAY DIFFRACTION	100
3.645-3.822	0.248	63	0.199	1590	X-RAY DIFFRACTION	100
3.822-4.028	0.298	95	0.192	1523	X-RAY DIFFRACTION	100
4.028-4.271	0.184	85	0.185	1416	X-RAY DIFFRACTION	100
4.271-4.565	0.229	63	0.174	1354	X-RAY DIFFRACTION	100
4.565-4.929	0.158	54	0.163	1246	X-RAY DIFFRACTION	100
4.929-5.396	0.197	49	0.174	1187	X-RAY DIFFRACTION	100
5.396-6.028	0.212	48	0.193	1040	X-RAY DIFFRACTION	100
6.028-6.951	0.261	42	0.223	949	X-RAY DIFFRACTION	100
6.951-8.489	0.215	47	0.194	776	X-RAY DIFFRACTION	100
8.489-11.907	0.163	44	0.151	593	X-RAY DIFFRACTION	100
11.907-29.746	0.316	17	0.206	324	X-RAY DIFFRACTION	92.9155

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	2.7024	0.0761	-1.1843	2.0409	0.2154	1.1843	0.0391	-0.091	-0.0194	-0.097	-0.124	-0.0756	-0.0477	0.0533	0.0849	0.5959	0.0755	0.0011	0.54	-0.0316	0.0176	56.203	-27.353	-17.119
2	1.8409	0.9188	-0.3992	3.4318	-0.1622	0.6928	0.0082	0.2618	-0.2442	-0.4283	-0.0992	0.252	0.0382	-0.2749	0.0911	0.6231	0.0605	-0.0454	0.5525	-0.0743	0.1086	34.966	-6.152	2.553
3	1.8385	0.1545	-0.4149	3.0826	0.7791	1.9908	0.0486	-0.17	0.2256	-0.0291	-0.1349	-0.0195	-0.1199	0.091	0.0864	0.5487	0.049	0.0477	0.5278	0.0339	0.0552	59.467	-29.438	19.559
4	1.9247	1.0861	-0.303	3.2128	-0.2056	0.7325	0.0389	-0.1883	0.1772	0.2102	-0.1016	-0.031	0.0009	0.2077	0.0628	0.6339	0.0716	0.0286	0.5377	0.0124	0.0536	88.039	-39.007	0.661

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	H	1 - 122
2	X-RAY DIFFRACTION	1	ALL	L	3 - 110
3	X-RAY DIFFRACTION	2	ALL	H	123 - 222
4	X-RAY DIFFRACTION	2	ALL	L	111 - 212
5	X-RAY DIFFRACTION	3	ALL	A	2 - 122
6	X-RAY DIFFRACTION	3	ALL	B	2 - 110
7	X-RAY DIFFRACTION	4	ALL	A	123 - 222
8	X-RAY DIFFRACTION	4	ALL	B	111 - 204

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