3EO0: GC-1008 Fab Light Chain

Structure of the Transforming Growth Factor-Beta Neutralizing Antibody GC-1008. Determined by X-ray diffraction at 1.75 Å resolution. Released 2 Dec 2008.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Mus musculus
Chains: 4
Atoms: 7,470
Mol. weight: 95.1 kDa
Released: 2 Dec 2008

Explore 3EO0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3EO0 contains 35 α-helices and 91 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: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	34-39	6	2
β-strand	46-50	5	2
β-strand	54-55	2	2
α-helix	56	1
β-strand	63-68	6	1
β-strand	71-76	6	1
α-helix	81-83	3
β-strand	85-91	7	2
α-helix	97	1
β-strand	98-99	2	2
β-strand	103-107	5	2
β-strand	112	1	3
α-helix	113-114	2
β-strand	115-119	5	4
α-helix	120-122	3
α-helix	123-127	5
β-strand	130-140	11	4
β-strand	141	1	3
β-strand	146-151	6	5
β-strand	154-155	2	5
α-helix	156	1
β-strand	160-164	5	4
α-helix	165-168	4
β-strand	174-183	10	4
α-helix	184-189	6
β-strand	192-198	7	5
β-strand	206-211	6	5

Chain B: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
α-helix	7-9	3
β-strand	10-12	3	7
β-strand	18-25	8	6
β-strand	34-39	6	7
β-strand	46-52	7	7
β-strand	57-60	4	7
β-strand	68-73	6	6
α-helix	74-76	3
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-99	8	7
β-strand	107-110	4	7
β-strand	114-118	5	7
α-helix	121-123	3
β-strand	124	1	8
α-helix	125-126	2
β-strand	127-131	5	9
β-strand	142-152	11	9
β-strand	153	1	8
β-strand	158-161	4	10
α-helix	162-164	3
β-strand	166	1	10
β-strand	170-172	3	9
α-helix	173-175	3
β-strand	176-177	2	9
β-strand	183-192	10	9
α-helix	193-195	3
β-strand	196	1	11
β-strand	199	1	11
β-strand	202-207	6	10
α-helix	208-210	3
β-strand	212-217	6	10

Chain C: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-13	4	13
β-strand	19-25	7	12
β-strand	34-39	6	13
β-strand	46-50	5	13
β-strand	54-55	2	13
α-helix	56	1
β-strand	63-68	6	12
β-strand	71-76	6	12
α-helix	81-83	3
β-strand	85-91	7	13
α-helix	97	1
β-strand	98-99	2	13
β-strand	103-107	5	13
β-strand	112	1	14
α-helix	113-114	2
β-strand	115-119	5	15
α-helix	120-122	3
α-helix	123-126	4
β-strand	130-140	11	15
β-strand	141	1	14
β-strand	146-151	6	16
β-strand	154-155	2	16
α-helix	156	1
β-strand	160-164	5	15
α-helix	165-168	4
β-strand	174-183	10	15
α-helix	184-189	6
β-strand	192-198	7	16
β-strand	206-211	6	16

Chain D: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	17
β-strand	10-12	3	18
β-strand	18-25	8	17
β-strand	34-39	6	18
β-strand	46-52	7	18
β-strand	57-60	4	18
β-strand	65	1	17
β-strand	68-73	6	17
α-helix	74-76	3
β-strand	78-83	6	17
α-helix	88-90	3
β-strand	92-99	8	18
β-strand	107-110	4	18
β-strand	114-118	5	18
α-helix	121-123	3
β-strand	124	1	19
α-helix	125-126	2
β-strand	127-131	5	20
β-strand	142-152	11	20
β-strand	153	1	19
β-strand	158-161	4	21
α-helix	162-164	3
β-strand	166	1	21
β-strand	170-172	3	20
α-helix	173-175	3
β-strand	176-177	2	20
β-strand	183-192	10	20
α-helix	193-195	3
β-strand	196	1	22
β-strand	199	1	22
β-strand	202-207	6	21
α-helix	208-210	3
β-strand	212-217	6	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GC-1008 Fab Light Chain	A, C	protein	215	Mus musculus	Q6PJF2 (AlphaFold model)
GC-1008 Fab Heavy Chain	B, D	protein	225	Mus musculus	P01861 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3EO0_1 GC-1008 Fab Light Chain (chains A, C)
ETVLTQSPGTLSLSPGERATLSCRASQSLGSSYLAWYQQKPGQAPRLLIYGASSRAPGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYADSPITFGQGTRLEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, D), FASTA

>3EO0_2 GC-1008 Fab Heavy Chain (chains B, D)
QVQLVQSGAEVKKPGSSVKVSCKASGYTFSSNVISWVRQAPGQGLEWMGGVIPIVDIANY
AQRFKGRVTITADESTSTTYMELSSLRSEDTAVYYCASTLGLVLDAMDYWGQGTLVTVSS
ASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVEPKYGPP

Primary citation

A cytokine-neutralizing antibody as a structural mimetic of 2 receptor interactions. Wilkinson, T., Turner, R., Podichetty, S. et al. Proc Natl Acad Sci U S A (2008) 105:20251-20256. DOI 10.1073/pnas.0807200106 · PubMed

Other PDB entries of the same protein (UniProt Q6PJF2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QH0 1.87 Å, Crystal structure of the SARS-CoV-2 RBD with the antibody Cv2.3194
1DN0 2.28 Å, Structure of the FAB fragment from a human IgM cold agglutinin
2AGJ 2.6 Å, Crystal Structure of a glycosylated Fab from an IgM cryoglobulin with properties of a…
8QH1 2.65 Å, Crystal structure of the SARS-CoV-2 RBD from the Omicron BA4 variant with the antibody…
1U6A 2.81 Å, Crystal Structure of the Broadly Neutralizing Anti-HIV Fab F105
1QLR 2.83 Å, Crystal structure of the FAB fragment of a human monoclonal IgM cold agglutinin
4YPG 3.0 Å, Structural Insights Into the Neutralization Properties of a Human Anti-Interferon…
3EO1 3.1 Å, Structure of the Fab Fragment of GC-1008 in Complex with Transforming Growth Factor-Beta 3
3B2V 3.3 Å, Crystal structure of the extracellular region of the epidermal growth factor receptor in…
6MYY 3.8 Å, Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs…
6UDK 3.9 Å, HIV-1 bNAb 1-55 in complex with modified BG505 SOSIP-based immunogen RC1 and 10-1074
6MZJ 4.8 Å, Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 2 Fabs…

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