5D4K: Human polymeric Ig receptor (pIgR) ectodomain

Crystal structure of the human polymeric Ig receptor (pIgR) ectodomain. Determined by X-ray diffraction at 2.6 Å resolution. Released 16 Mar 2016.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 8,530
Mol. weight: 125.41 kDa
Ligands: NAG
Released: 16 Mar 2016

Explore 5D4K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D4K contains 33 α-helices and 93 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: 16 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
β-strand	9-13	5	2
β-strand	18-23	6	1
α-helix	29-31	3
α-helix	34	1
β-strand	35-40	6	2
α-helix	42-44	3
β-strand	46-51	6	2
β-strand	56	1	2
β-strand	64-69	6	1
β-strand	74-79	6	1
α-helix	84-86	3
β-strand	88-94	7	2
β-strand	102-110	9	2
β-strand	119-125	7	3
β-strand	130-135	6	4
α-helix	138-140	3
β-strand	145-150	6	3
β-strand	155-160	6	3
β-strand	165	1	3
β-strand	173-177	5	4
β-strand	184-189	6	4
α-helix	194-196	3
β-strand	198-204	7	3
β-strand	211-220	10	3
α-helix	221-224	4
β-strand	225-230	6	5
β-strand	235-239	5	6
β-strand	250-255	6	5
β-strand	261-266	6	5
β-strand	271	1	5
α-helix	273-275	3
β-strand	279-281	3	6
α-helix	282-285	4
β-strand	290-294	5	6
α-helix	299-301	3
β-strand	304-309	6	5
β-strand	321-329	9	5
α-helix	337-338	2
β-strand	339-343	5	7
β-strand	348-354	7	8
α-helix	357-359	3
α-helix	363-364	2
β-strand	365-368	4	7
β-strand	379-382	4	7
β-strand	387	1	7
α-helix	389-391	3
β-strand	395-401	7	8
β-strand	405-411	7	8
α-helix	415-417	3
β-strand	419-424	6	7
β-strand	433-439	7	7
β-strand	447	1	9
β-strand	451-455	5	10
β-strand	460-466	7	9
β-strand	474-479	6	10
β-strand	486-487	2	10
β-strand	490-492	3	9
β-strand	507-513	7	9
α-helix	518-520	3
β-strand	522-530	9	10
β-strand	533-545	13	10

Chain B: 17 helices, 47 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	11
β-strand	9-13	5	12
β-strand	18-23	6	11
α-helix	29-31	3
α-helix	34	1
β-strand	35-40	6	12
α-helix	42-44	3
β-strand	46-51	6	12
β-strand	56	1	12
β-strand	64-69	6	11
β-strand	74-79	6	11
α-helix	84-86	3
β-strand	88-94	7	12
β-strand	102-110	9	12
β-strand	114	1	3
β-strand	119-125	7	13
β-strand	130-135	6	14
α-helix	138-140	3
β-strand	145-151	7	13
β-strand	154-160	7	13
β-strand	165	1	13
β-strand	173-177	5	14
β-strand	184-189	6	14
α-helix	194-196	3
β-strand	198-204	7	13
β-strand	211-220	10	13
α-helix	221-224	4
β-strand	225-230	6	15
β-strand	235-239	5	16
β-strand	250-255	6	15
β-strand	261-266	6	15
β-strand	271	1	15
α-helix	273-275	3
β-strand	279-281	3	16
α-helix	282-284	3
β-strand	290-294	5	16
α-helix	299-301	3
β-strand	304-309	6	15
β-strand	321-329	9	15
α-helix	337-338	2
β-strand	339-343	5	17
β-strand	348-354	7	18
α-helix	359-361	3
α-helix	363-364	2
β-strand	365-368	4	17
β-strand	379-382	4	17
β-strand	387	1	17
α-helix	389-391	3
β-strand	395-401	7	18
β-strand	405-411	7	18
α-helix	415-417	3
β-strand	419-424	6	17
β-strand	433-439	7	17
β-strand	447	1	19
β-strand	451-455	5	20
β-strand	460-466	7	19
β-strand	474-479	6	20
α-helix	485	1
β-strand	486-487	2	20
β-strand	490-492	3	19
β-strand	507-513	7	19
α-helix	518-520	3
β-strand	522-530	9	20
β-strand	533-545	13	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymeric immunoglobulin receptor	A, B	protein	557	Homo sapiens	P01833 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5D4K_1 Polymeric immunoglobulin receptor (chains A, B)
KSPIFGPEEVNSVEGNSVSITCYYPPTSVNRHTRKYWCRQGARGGCITLISSEGYVSSKY
AGRANLTNFPENGTFVVNIAQLSQDDSGRYKCGLGINSRGLSFDVSLEVSQGPGLLNDTK
VYTVDLGRTVTINCPFKTENAQKRKSLYKQIGLYPVLVIDSSGYVNPNYTGRIRLDIQGT
GQLLFSVVINQLRLSDAGQYLCQAGDDSNSNKKNADLQVLKPEPELVYEDLRGSVTFHCA
LGPEVANVAKFLCRQSSGENCDVVVNTLGKRAPAFEGRILLNPQDKDGSFSVVITGLRKE
DAGRYLCGAHSDGQLQEGSPIQAWQLFVNEESTIPRSPTVVKGVAGSSVAVLCPYNRKES
KSIKYWCLWEGAQNGRCPLLVDSEGWVKAQYEGRLSLLEEPGNGTFTVILNQLTSRDAGF
YWCLTNGDTLWRTTVEIKIIEGEPNLKVPGNVTAVLGETLKVPCHFPCKFSSYEKYWCKW
NNTGCQALPSQDEGPSKAFVNCDENSRLVSLTLNLVTRADEGWYWCGVKQGHFYGETAAV
YVAVEERGSWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Water and common crystallization additives (SO4) are not listed.

Primary citation

The structure and dynamics of secretory component and its interactions with polymeric immunoglobulins. Stadtmueller, B.M., Huey-Tubman, K.E., Lopez, C.J. et al. Elife (2016) 5. DOI 10.7554/eLife.10640 · PubMed

Other PDB entries of the same protein (UniProt P01833 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1XED 1.9 Å, Crystal Structure of a Ligand-Binding Domain of the Human Polymeric Ig Receptor, pIgR
6UE7 2.9 Å, Structure of dimeric sIgA complex
6UE9 2.9 Å, Structure of tetrameric sIgA complex (Class 2)
6UE8 3.0 Å, Structure of tetrameric sIgA complex (Class 1)
6UEA 3.0 Å, Structure of pentameric sIgA complex
8SKV 3.1 Å, Structure of human SIgA1 in complex with Streptococcus pyogenes protein M4 (Arp4)
6LX3 3.15 Å, Cryo-EM structure of human secretory immunoglobulin A
7YSG 3.18 Å, Cryo-EM structure of human FcmR bound to sIgM
8SKU 3.2 Å, Structure of human SIgA1 in complex with human CD89 (FcaR1)
6LXW 3.27 Å, Cryo-EM structure of human secretory immunoglobulin A in complex with the N-terminal…
7K0C 3.3 Å, Structure of Secretory IgM Core
6KXS 3.4 Å, Cryo-EM structure of human IgM-Fc in complex with the J chain and the ectodomain of pIgR

Browse structure collections

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