3EO1: Fab Fragment of GC-1008

Structure of the Fab Fragment of GC-1008 in Complex with Transforming Growth Factor-Beta 3. Determined by X-ray diffraction at 3.1 Å resolution. Released 2 Dec 2008.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Mus musculus, Homo sapiens
Chains: 12
Atoms: 16,556
Mol. weight: 240 kDa
Released: 2 Dec 2008

Explore 3EO1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3EO1 contains 64 α-helices and 220 β-strands across 12 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.

Chains A and G: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
α-helix	18	1
β-strand	19-29	11	1
β-strand	34-39	6	2
β-strand	46-51	6	2
β-strand	54-55	2	2
β-strand	63-76	14	1
α-helix	81-83	3
β-strand	86-91	6	2
β-strand	94	1	3
α-helix	97	1
β-strand	98-99	2	2
β-strand	104-107	4	2
β-strand	112	1	4
β-strand	116-118	3	5
α-helix	120-122	3
α-helix	123-126	4
β-strand	132-140	9	5
β-strand	141	1	4
β-strand	146-151	6	6
β-strand	161-164	4	5
β-strand	174-181	8	5
α-helix	184-187	4
β-strand	193-198	6	6
β-strand	206	1	6
β-strand	209-210	2	6

Chains B and H: 2 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	7
β-strand	10-12	3	8
β-strand	18-24	7	7
β-strand	34-39	6	8
β-strand	45-52	8	8
β-strand	57-60	4	8
α-helix	62-64	3
β-strand	68-73	6	7
β-strand	78-83	6	7
β-strand	92-99	8	8
β-strand	107-110	4	8
β-strand	115-118	4	8
β-strand	128-131	4	9
β-strand	142-149	8	9
β-strand	152	1	10
β-strand	157-158	2	11
β-strand	170-172	3	9
α-helix	173-175	3
β-strand	176-177	2	10
β-strand	183-184	2	10
β-strand	187-192	6	9
β-strand	203-207	5	11
β-strand	212-216	5	11

Chains C and I: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	12
α-helix	4-7	4
β-strand	16-18	3	13
β-strand	22-23	2	14
α-helix	24-28	5
β-strand	33-35	3	12
β-strand	38-39	2	14
β-strand	43-45	3	13
β-strand	54	1	12
α-helix	57-68	12
α-helix	70-72	3
α-helix	75-77	3
β-strand	78-91	14	12
β-strand	93	1	3
β-strand	96-111	16	12

Chains D and J: 8 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	15
β-strand	10	1	16
β-strand	13	1	17
α-helix	18	1
β-strand	19-23	5	15
β-strand	34-39	6	16
β-strand	46-49	4	16
β-strand	55	1	16
α-helix	56	1
β-strand	63-64	2	15
β-strand	67-68	2	15
β-strand	71-76	6	15
α-helix	81-83	3
β-strand	86-91	6	16
α-helix	97	1
β-strand	98-99	2	16
β-strand	103-104	2	16
α-helix	106	1
β-strand	107	1	17
α-helix	108	1
β-strand	112	1	18
β-strand	117-118	2	19
β-strand	132-134	3	20
β-strand	135-136	2	19
β-strand	140	1	21
β-strand	141	1	18
β-strand	145-148	4	22
β-strand	151	1	22
β-strand	161-164	4	20
α-helix	165-168	4
β-strand	174	1	21
β-strand	176-181	6	20
α-helix	184-187	4
β-strand	192-199	8	22
β-strand	207-211	5	22

Chains E and K: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	23
α-helix	7-9	3
β-strand	10-12	3	24
β-strand	18-24	7	23
β-strand	34-39	6	24
β-strand	45-52	8	24
β-strand	57-60	4	24
α-helix	62-64	3
β-strand	68	1	23
β-strand	71	1	23
β-strand	78-83	6	23
β-strand	92-98	7	24
β-strand	109-110	2	24
β-strand	115-118	4	24
β-strand	124	1	25
β-strand	127-131	5	26
β-strand	144-152	9	26
β-strand	153	1	25
β-strand	158-159	2	27
α-helix	162-164	3
β-strand	171-172	2	26
α-helix	173-175	3
β-strand	177	1	26
β-strand	183-190	8	26
α-helix	193-195	3
β-strand	205-207	3	27
β-strand	212-214	3	27

Chains F and L: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	28
α-helix	4-7	4
β-strand	16-18	3	29
α-helix	19	1
β-strand	21-23	3	30
α-helix	24-28	5
β-strand	35	1	28
β-strand	38-40	3	30
β-strand	43-45	3	29
β-strand	54	1	28
α-helix	57-68	12
α-helix	70-72	3
α-helix	75-77	3
β-strand	78-92	15	28
β-strand	95-111	17	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GC-1008 Fab Light Chain	A, D, G, J	protein	215	Mus musculus	Q6PJF2 (AlphaFold model)
GC-1008 Fab Heavy Chain	B, E, H, K	protein	225	Mus musculus	P01861 (AlphaFold model)
Transforming growth factor beta-3	C, F, I, L	protein	112	Homo sapiens	P10600 (AlphaFold model)

Sequence of entity 1 (A, D, G, J), FASTA

>3EO1_1 GC-1008 Fab Light Chain (chains A, D, G, J)
ETVLTQSPGTLSLSPGERATLSCRASQSLGSSYLAWYQQKPGQAPRLLIYGASSRAPGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYADSPITFGQGTRLEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, E, H, K), FASTA

>3EO1_2 GC-1008 Fab Heavy Chain (chains B, E, H, K)
QVQLVQSGAEVKKPGSSVKVSCKASGYTFSSNVISWVRQAPGQGLEWMGGVIPIVDIANY
AQRFKGRVTITADESTSTTYMELSSLRSEDTAVYYCASTLGLVLDAMDYWGQGTLVTVSS
ASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKYGPP

Sequence of entity 3 (C, F, I, L), FASTA

>3EO1_3 Transforming growth factor beta-3 (chains C, F, I, L)
ALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPYLRSADTTHST
VLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQLSNMVVKSCKCS

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:

3EO0 1.75 Å, Structure of the Transforming Growth Factor-Beta Neutralizing Antibody GC-1008
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…
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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