1ADQ: Human IgM rheumatoid factor FAB

Crystal structure of a human IgM rheumatoid factor FAB in complex with its autoantigen IgG fc. Determined by X-ray diffraction at 3.15 Å resolution. Released 16 Sept 1998.

Method: X-ray diffraction
Resolution: 3.15 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,977
Mol. weight: 70.72 kDa
Released: 16 Sept 1998

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

Secondary structure: helices and β-sheets

1ADQ contains 22 α-helices and 73 β-strands across 3 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: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	239-243	5	1
α-helix	244-246	3
α-helix	247-251	5
β-strand	258-264	7	1
β-strand	270	1	2
β-strand	275	1	3
β-strand	278-279	2	3
β-strand	282-283	2	3
β-strand	288	1	1
β-strand	296	1	4
β-strand	299	1	4
β-strand	304-307	4	1
α-helix	310-314	5
β-strand	319-323	5	3
β-strand	326	1	2
β-strand	328	1	2
β-strand	332-336	5	3
β-strand	344	1	5
β-strand	347-351	5	6
α-helix	352-354	3
α-helix	357-359	3
β-strand	362-372	11	6
β-strand	373	1	5
β-strand	378-382	5	7
β-strand	387	1	7
β-strand	391-393	3	6
α-helix	394-396	3
β-strand	397-398	2	6
β-strand	404-413	10	6
α-helix	414-418	5
β-strand	423-428	6	7
β-strand	437-441	5	7

Chain H: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	15
β-strand	11-12	2	16
β-strand	18-25	8	15
α-helix	29-31	3
β-strand	34-39	6	17
β-strand	45-51	7	17
β-strand	57-59	3	17
β-strand	67-72	6	15
α-helix	73-75	3
β-strand	77-82	6	15
α-helix	84-86	3
β-strand	88-94	7	17
β-strand	102-103	2	17
β-strand	107-109	3	17
β-strand	110-111	2	16
β-strand	117	1	18
α-helix	118-119	2
β-strand	120-125	6	19
β-strand	140-147	8	19
β-strand	148	1	18
β-strand	153-158	5	20
β-strand	172-173	2	19
β-strand	177-179	3	19
β-strand	184-191	8	19
β-strand	206-212	6	20
β-strand	218-223	5	20

Chain L: 11 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	8
β-strand	9-13	4	9
α-helix	18	1
β-strand	19-25	7	8
α-helix	28-30	3
β-strand	34-38	5	9
β-strand	45-48	4	9
β-strand	49	1	10
β-strand	53	1	10
β-strand	62-63	2	8
β-strand	66-67	2	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	85-92	8	9
β-strand	95B-98	4	9
α-helix	99	1
β-strand	102-106	5	9
α-helix	109-110	2
β-strand	111	1	11
α-helix	112-113	2
β-strand	114-118	5	12
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-139	10	12
β-strand	140	1	11
β-strand	145-150	6	13
β-strand	153-154	2	13
α-helix	155	1
β-strand	159-161	3	12
α-helix	162-164	3
β-strand	165	1	14
β-strand	173	1	12
β-strand	174	1	14
β-strand	175-181	7	12
α-helix	183-187	5
β-strand	192-198	7	13
β-strand	203-209	7	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IGG4 rea fc	A	protein	206	Homo sapiens	P01861 (AlphaFold model)
IgM-lambda rf-an FAB (light chain)	L	protein	213	Homo sapiens
IgM-lambda rf-an FAB (heavy chain)	H	protein	225	Homo sapiens

Sequence of entity 1 (A), FASTA

>1ADQ_1 IGG4 REA FC (chains A)
PSVFLFPPKPKDTLMISRTPEVTCVVVDVSQEDPQVQFNWYVDGVQVHNAKTKPREQQFN
STYRVVSVLTVLHQNWLDGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLPPSQEE
MTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRW
QEGNVFSCSVMHEALHNHYTQKSLSL

Sequence of entity 2 (L), FASTA

>1ADQ_2 IGM-LAMBDA RF-AN FAB (LIGHT CHAIN) (chains L)
YVLTQPPSVSVAPGQTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPPGIPERF
SGSNSGNTATLTISRVEAGDEADYYCQVWDSSSDHAVFGGGTKLTVLGQPKAAPSVTLFP
PSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTTPSKQSNNKYAASSYLS
LTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (H), FASTA

>1ADQ_3 IGM-LAMBDA RF-AN FAB (HEAVY CHAIN) (chains H)
EVQLVESGGGLVQPGRSLRLSCVTSGFTFDDYAMHWVRQSPGKGLEWVSGISWNTGTIIY
ADSVKGRFIISRDNAKNSLYLQMNSLRVEDTALYYCAKTRSYVVAAEYYFHYWGQGILVT
VSSGSASAPTLFPLVSCENSNPSSTVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPS
VLRGGKYAATSQVLLPSKDVMQGTNEHVVCKVQHPNGNKEKDVPL

Primary citation

Structure of human IgM rheumatoid factor Fab bound to its autoantigen IgG Fc reveals a novel topology of antibody-antigen interaction. Corper, A.L., Sohi, M.K., Bonagura, V.R. et al. Nat Struct Biol (1997) 4:374-381. DOI 10.1038/nsb0597-374 · PubMed

Other PDB entries of the same protein (UniProt P01861 (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
4B53 1.8 Å, Crystal structure of the isolated IgG4 CH3 domain
5W5N 1.85 Å, Crystal structure of human IgG4-Sigma2 Fc fragment
4C54 1.9 Å, Crystal structure of recombinant human IgG4 Fc
5W5M 1.9 Å, Crystal structure of human IgG4-Sigma1 Fc fragment
5HVW 1.95 Å, Monomeric IgG4 Fc
3X3F 2.1 Å, TRAIL-R2 Extracellular Region Complexed to a Fab fragment from Human Agonist Antibody…
6WMH 2.3 Å, Next generation monomeric IgG4 Fc
4C55 2.35 Å, Crystal structure of serum-derived human IgG4 Fc
6WNA 2.4 Å, Next generation monomeric IgG4 Fc
6WOL 2.49 Å, Next generation monomeric IgG4 Fc bound to neonatal Fc receptor
3X3G 2.51 Å, Fab fragment from anti TRAIL-R2 Human Agonist Antibody KMTR2

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