1DN0: FAB fragment from a human IgM cold agglutinin

Structure of the FAB fragment from a human IgM cold agglutinin. Determined by X-ray diffraction at 2.28 Å resolution. Released 24 Jan 2001.

Method: X-ray diffraction
Resolution: 2.28 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,208
Mol. weight: 96.87 kDa
Released: 24 Jan 2001

Explore 1DN0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1DN0 contains 29 α-helices and 87 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: 11 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
α-helix	30-32	3
β-strand	34-39	6	2
α-helix	44-45	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	86-91	6	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	154-156	3	5
β-strand	160-164	5	4
α-helix	165-168	4
β-strand	174-183	10	4
α-helix	184-188	5
β-strand	192-198	7	5
β-strand	206-211	6	5

Chain B: 3 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
α-helix	32-33	2
β-strand	34-39	6	8
β-strand	46-51	6	8
β-strand	57-59	3	8
β-strand	67-72	6	6
β-strand	77-82	6	6
α-helix	87-89	3
β-strand	91-97	7	8
β-strand	109-110	2	8
β-strand	114-116	3	8
β-strand	117-118	2	7
β-strand	124	1	9
β-strand	127-132	6	10
β-strand	144-153	10	10
β-strand	154	1	9
β-strand	159-164	6	11
β-strand	169-170	2	11
β-strand	173-175	3	10
α-helix	176-178	3
β-strand	179-181	3	10
β-strand	184-193	10	10
β-strand	205-211	7	11
β-strand	217-222	6	11

Chain C: 10 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
α-helix	30-32	3
β-strand	34-39	6	13
α-helix	44-45	2
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	86-91	6	13
α-helix	97	1
β-strand	98-99	2	13
β-strand	103-107	5	13
β-strand	112	1	14
β-strand	115-119	5	15
α-helix	120-122	3
α-helix	123-127	5
β-strand	130-140	11	15
β-strand	141	1	14
β-strand	145-151	7	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	184-188	5
β-strand	192-199	8	16
β-strand	206-211	6	16

Chain D: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	17
β-strand	11-12	2	18
β-strand	18-25	8	17
α-helix	33	1
β-strand	34-39	6	19
β-strand	46-51	6	19
β-strand	57-59	3	19
β-strand	67-72	6	17
β-strand	77-82	6	17
α-helix	87-89	3
β-strand	91-97	7	19
β-strand	109-110	2	19
β-strand	114-116	3	19
β-strand	117-118	2	18
β-strand	124	1	20
β-strand	127-132	6	21
β-strand	144-153	10	21
β-strand	154	1	20
β-strand	159-164	6	22
α-helix	168	1
β-strand	169-170	2	22
α-helix	175-178	4
β-strand	179-181	3	21
β-strand	184-193	10	21
α-helix	195-198	4
β-strand	205-211	7	22
β-strand	217-222	6	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IgM-kappa cold agglutinin (light chain)	A, C	protein	215	Homo sapiens	Q6PJF2 (AlphaFold model)
IgM-kappa cold agglutinin (heavy chain)	B, D	protein	232	Homo sapiens	P01871 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>1DN0_1 IGM-KAPPA COLD AGGLUTININ (LIGHT CHAIN) (chains A, C)
EIVLTQSPATLSLSPGERATLSCGASQSVSSNYLAWYQQKPGQAPRLLIYDASSRATGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPLTFGGGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, D), FASTA

>1DN0_2 IGM-KAPPA COLD AGGLUTININ (HEAVY CHAIN) (chains B, D)
EVQLQQWGAGLLKPSETLSLTCAVYGGSFSDYYWSWIRQPPGKGLEWIGEINHSGSTNYN
PSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARPPHDTSGHYWNYWGQGTLVTVSS
GSASAPTLFPLVSCENSPSDTSSVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVL
RGGKYAATSQVLLPSKDVMAGTDEHVVCKVQHPNGNKEKNVPLPVIAELPPK

Primary citation

Three-dimensional structure of the Fab from a human IgM cold agglutinin. Cauerhff, A., Braden, B.C., Carvalho, J.G. et al. J Immunol (2000) 165:6422-6428. 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
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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