5W5M: Human IgG4-Sigma1 Fc fragment

Crystal structure of human IgG4-Sigma1 Fc fragment. Determined by X-ray diffraction at 1.9 Å resolution. Released 13 Sept 2017.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,771
Mol. weight: 53.55 kDa
Released: 13 Sept 2017

Explore 5W5M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W5M contains 23 α-helices and 39 β-strands across 2 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: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	240-243	4	1
α-helix	244-246	3
α-helix	247-251	5
β-strand	258-266	9	1
α-helix	270-272	3
β-strand	273-279	7	2
β-strand	282-284	3	2
β-strand	288-294	7	1
β-strand	300-307	8	1
α-helix	310-314	5
β-strand	319-325	7	2
β-strand	332-336	5	2
α-helix	338-340	3
β-strand	344	1	3
α-helix	345-346	2
β-strand	347-351	5	4
α-helix	352-354	3
α-helix	355-357	3
β-strand	362-372	11	4
β-strand	373	1	3
β-strand	378-383	6	5
β-strand	386-387	2	5
α-helix	388	1
β-strand	391-393	3	4
α-helix	394-396	3
β-strand	397-398	2	4
β-strand	404-413	10	4
α-helix	414-418	5
β-strand	423-428	6	5
α-helix	433-435	3
β-strand	436-441	6	5

Chain B: 11 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	237-239	3
β-strand	240-243	4	6
α-helix	244-246	3
α-helix	247-251	5
β-strand	258-266	9	6
β-strand	273-279	7	7
β-strand	282-284	3	7
β-strand	288-289	2	6
α-helix	290-292	3
β-strand	293-295	3	6
β-strand	299-307	9	6
α-helix	310-314	5
β-strand	319-325	7	7
β-strand	332-336	5	7
α-helix	338-340	3
β-strand	344	1	8
α-helix	345-346	2
β-strand	347-351	5	9
α-helix	355-359	5
β-strand	362-372	11	9
β-strand	373	1	8
β-strand	378-383	6	10
β-strand	386-387	2	10
β-strand	391-393	3	9
α-helix	394-396	3
β-strand	397-398	2	9
β-strand	404-413	10	9
α-helix	414-418	5
β-strand	423-428	6	10
α-helix	433-435	3
β-strand	436-441	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin heavy constant gamma 4	A, B	protein	223	Homo sapiens	P01861 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5W5M_1 Immunoglobulin heavy constant gamma 4 (chains A, B)
TCPPCPAPEAAGASSVFLFPPKPKDTLMISRTPEVTCVVVDVSQEDPEVQFNWYVDGVEV
HNAKTKPREEQFNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPR
EPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSF
FLYSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSLSLGK

Primary citation

Functional, Biophysical, and Structural Characterization of Human IgG1 and IgG4 Fc Variants with Ablated Immune Functionality. Tam, S.H., McCarthy, S.G., Armstrong, A.A. et al. Antibodies (Basel) (2017) 6. DOI 10.3390/antib6030012 · 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
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
6WIB 2.55 Å, Next generation monomeric IgG4 Fc

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