4D2N: Deglycosylated serum-derived human IgG4 Fc

Crystal structure of deglycosylated serum-derived human IgG4 Fc. Determined by X-ray diffraction at 2.7 Å resolution. Released 2 Jul 2014.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 6,328
Mol. weight: 101.89 kDa
Released: 2 Jul 2014

Explore 4D2N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4D2N contains 40 α-helices and 77 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, 19 β-strands

Element	Residues	Length	Sheet
β-strand	239-243	5	1
α-helix	244-246	3
α-helix	247-250	4
β-strand	258-266	9	1
β-strand	274-279	6	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	319-324	6	2
β-strand	332-336	5	2
α-helix	338-340	3
β-strand	344	1	3
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	386-388	3	5
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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	239-243	5	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	288-294	7	6
β-strand	300-307	8	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	352-354	3
α-helix	355-359	5
β-strand	362-372	11	9
β-strand	373	1	8
β-strand	378-383	6	10
β-strand	386-388	3	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

Chain C: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	239-243	5	11
α-helix	244-246	3
α-helix	247-251	5
β-strand	258-266	9	11
β-strand	274-279	6	12
β-strand	282-284	3	12
β-strand	287-289	3	11
β-strand	293-294	2	11
β-strand	300-307	8	11
α-helix	310-314	5
β-strand	319-324	6	12
β-strand	331-336	6	12
α-helix	338-340	3
β-strand	344	1	13
α-helix	345-346	2
β-strand	347-351	5	14
α-helix	352-354	3
α-helix	355-359	5
β-strand	362-372	11	14
β-strand	373	1	13
β-strand	378-383	6	15
β-strand	386-388	3	15
β-strand	391-393	3	14
α-helix	394-396	3
β-strand	397-398	2	14
β-strand	404-413	10	14
α-helix	414-418	5
β-strand	423-428	6	15
α-helix	433-435	3
β-strand	437-441	5	15

Chain D: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	239-243	5	16
α-helix	244-246	3
α-helix	247-251	5
β-strand	258-266	9	16
β-strand	273-279	7	17
β-strand	282-284	3	17
β-strand	288-294	7	16
β-strand	300-307	8	16
α-helix	310-314	5
β-strand	319-325	7	17
β-strand	332-336	5	17
α-helix	338-340	3
β-strand	344	1	18
α-helix	345-346	2
β-strand	347-351	5	19
α-helix	352-354	3
α-helix	357-359	3
β-strand	362-372	11	19
β-strand	373	1	18
β-strand	378-383	6	20
β-strand	386-387	2	20
α-helix	388	1
β-strand	391-393	3	19
α-helix	394-396	3
β-strand	397-398	2	19
β-strand	404-413	10	19
α-helix	414-418	5
β-strand	423-428	6	20
α-helix	433-435	3
β-strand	437-441	5	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ig gamma-4 chain C region	A, B, C, D	protein	226	HOMO SAPIENS	P01861 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>4D2N_1 IG GAMMA-4 CHAIN C REGION (chains A, B, C, D)
YGPPCPSCPAPEFLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSQEDPEVQFNWYVDG
VEVHNAKTKPREEQFDSTYRVVSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKG
QPREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSD
GSFFLYSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSLSLGK

Primary citation

Crystal Structure of Deglycosylated Human Igg4-Fc. Davies, A.M., Jefferis, R., Sutton, B.J. Mol Immunol (2014) 62:46. DOI 10.1016/J.MOLIMM.2014.05.015 · 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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