8ECV: Bovine Fab 2F12

Bovine Fab 2F12. Determined by X-ray diffraction at 1.81 Å resolution. Released 20 Sept 2023.

Method: X-ray diffraction
Resolution: 1.81 Å
Organisms: Bos taurus, Homo sapiens
Chains: 4
Atoms: 7,554
Mol. weight: 101.72 kDa
Released: 20 Sept 2023

Explore 8ECV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ECV contains 43 α-helices and 102 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	15
β-strand	5	1	16
β-strand	9-14	5	17
β-strand	19-24	6	16
α-helix	28-30	3
β-strand	34-38	5	17
β-strand	45-49	5	17
β-strand	53-54	2	17
α-helix	55	1
β-strand	62-67	6	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	84-91	8	17
β-strand	96-98	3	17
β-strand	99	1	15
β-strand	102-106A	6	17
α-helix	108-110	3
β-strand	111	1	18
α-helix	112-113	2
β-strand	114-118	5	19
α-helix	122-125	4
β-strand	130-139	10	19
β-strand	140	1	18
β-strand	145-150	6	20
β-strand	153-155	3	20
β-strand	159-161	3	19
α-helix	162-164	3
β-strand	165-166	2	19
β-strand	172-180	9	19
α-helix	182-187	6
β-strand	191-197	7	20
β-strand	200-206	7	20

Chain B: 14 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	21
β-strand	11-12	2	22
β-strand	18-25	8	21
α-helix	29-31	3
β-strand	33-39	7	23
β-strand	45-51	7	23
β-strand	57-59	3	23
α-helix	61-66	6
β-strand	67-72	6	21
α-helix	73-75	3
β-strand	77-82	6	21
α-helix	84-86	3
β-strand	88-101	14	23
β-strand	107-110	4	24
β-strand	118-121	4	24
α-helix	133-135	3
β-strand	138-139	2	24
β-strand	145-154	10	23
β-strand	158-160	3	23
β-strand	171-172	2	22
α-helix	176-177	2
β-strand	178	1	25
α-helix	179-180	2
β-strand	181-185	5	26
α-helix	186-188	3
α-helix	189-191	3
β-strand	196-206	11	26
β-strand	207	1	25
β-strand	212-215	4	27
α-helix	216-218	3
β-strand	220	1	27
β-strand	224-226	3	26
α-helix	227-229	3
β-strand	230-231	2	26
α-helix	232	1
β-strand	237-246	10	26
α-helix	247-249	3
β-strand	255-261	7	27
α-helix	262-264	3
β-strand	266-272	7	27

Chain H: 12 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	33-39	7	9
β-strand	45-51	7	9
β-strand	57-59	3	9
α-helix	64-66	3
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-101	14	9
β-strand	107-110	4	10
β-strand	118-121	4	10
α-helix	133-135	3
β-strand	138-139	2	10
β-strand	145-154	10	9
β-strand	158-160	3	9
β-strand	171-172	2	8
α-helix	176-177	2
β-strand	178	1	11
α-helix	179-180	2
β-strand	181-185	5	12
α-helix	186-188	3
α-helix	189-192	4
β-strand	196-206	11	12
β-strand	207	1	11
β-strand	212-215	4	13
α-helix	216-218	3
β-strand	220	1	13
β-strand	224-226	3	12
α-helix	227-229	3
β-strand	230-231	2	12
β-strand	237-246	10	12
α-helix	247-249	3
β-strand	250	1	14
β-strand	253	1	14
β-strand	256-261	6	13
α-helix	262-264	3
β-strand	266-271	6	13

Chain L: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	5	1	2
β-strand	9-14	5	3
β-strand	19-24	6	2
α-helix	28-30	3
β-strand	34-38	5	3
β-strand	45-49	5	3
β-strand	53-54	2	3
α-helix	55	1
β-strand	62-67	6	2
β-strand	70-75	6	2
α-helix	80-82	3
β-strand	84-91	8	3
β-strand	96-98	3	3
β-strand	99	1	1
β-strand	102-106A	6	3
α-helix	108-110	3
β-strand	111	1	4
α-helix	112-113	2
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-125	4
β-strand	130-139	10	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-155	3	6
β-strand	159-161	3	5
α-helix	162-164	3
β-strand	165-166	2	5
β-strand	172-180	9	5
α-helix	182-187	6
β-strand	191-197	7	6
β-strand	200-206	7	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
2F12 Fab Light chain	A, L	protein	216	Bos taurus, Homo sapiens	P0DOY2 (AlphaFold model)
2F12 Fab Heavy chain	B, H	protein	269	Bos taurus, Homo sapiens	P0DOX5 (AlphaFold model)

Sequence of entity 1 (A, L), FASTA

>8ECV_1 2F12 Fab Light chain (chains A, L)
QAVLNQPSSVSGSLGQRVSITCSGSSSNVGNGYVSWYQLIPGSAPRTLIYGDTSRASGVP
DRFSGSRSGNTATLTISSLQAEDEADYFCASAEDSSSNAVFGSGTTLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 2 (B, H), FASTA

>8ECV_2 2F12 Fab Heavy chain (chains B, H)
QVQLRESGPSLVKPSQTLSLTCTVSGFSLSDKAVGWVRRAPGKALEWLGSIDTGGMTGYN
PGLKSRLSITKDNSKSQVSLSVNSVTTEDSATYYCATVDQKTKNACPDDFDYRCSCIGGC
GCARKGCVGPLCCRSDLGGYLTDSPAYIYEWYIDLWGQGLLVTVSSASTKGPSVFPLAPS
SKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSS
SLGTQTYICNVNHKPSNTKVDKKVEPKSC

Primary citation

The smallest functional antibody fragment: Ultralong CDR H3 antibody knob regions potently neutralize SARS-CoV-2. Huang, R., Warner Jenkins, G., Kim, Y. et al. Proc Natl Acad Sci U S A (2023) 120:e2303455120-e2303455120. DOI 10.1073/pnas.2303455120 · PubMed

Other PDB entries of the same protein (UniProt P0DOY2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LLD 1.19 Å, Structure of wild-type IgG1 antibody heavy chain constant domain 1 and light chain…
3TV3 1.29 Å, Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with…
4LLQ 1.42 Å, Structure of redesigned IgG1 first constant and lambda domains (CH1:Clambda constant…
4LLY 1.6 Å, Crystal structure of Pertuzumab Clambda Fab with variable and constant domain redesigns…
3TWC 1.65 Å, Crystal structure of broad and potent HIV-1 neutralizing antibody PGT127 in complex with…
4LLM 1.75 Å, Structure of redesigned IgG1 first constant and lambda domains (CH1:Clambda constant…
1AQK 1.84 Å, Three-dimensional structure of a human FAB with high affinity for tetanus toxoid
1JVK 1.94 Å, Three-dimensional structure of an immunoglobulin light chain dimer acting as a lethal…
4LLW 1.95 Å, Crystal structure of Pertuzumab Clambda Fab with variable domain redesign (VRD2) at 1.95A
4EOW 1.97 Å, Crystal structure of a disease-associated anti-human GM-CSF autoantibody MB007
7FAB 2.0 Å, Crystal structure of human immunoglobulin fragment FAB new refined at 2.0 Å resolution
8ECQ 2.0 Å, Bovine Fab 2G3

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