8XJ4: Prostatic acid phosphatase in human semen

Structure of prostatic acid phosphatase in human semen. Determined by electron microscopy at 3.19 Å resolution. Released 28 Feb 2024.

Method: Electron microscopy
Resolution: 3.19 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,820
Mol. weight: 82.93 kDa
Ligands: NAG, MAN
Released: 28 Feb 2024

Explore 8XJ4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8XJ4 contains 39 α-helices and 20 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: 18 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	34-42	9	3
β-strand	47	1	4
β-strand	70	1	4
α-helix	72-88	17
β-strand	102-105	4	3
α-helix	110-123	14
α-helix	128-130	3
β-strand	144	1	3
α-helix	162-173	12
α-helix	175-181	7
α-helix	186-195	10
α-helix	202-205	4
α-helix	206-210	5
α-helix	211-218	8
α-helix	221-224	4
α-helix	229-247	19
α-helix	252-255	4
α-helix	256-260	5
α-helix	261-276	16
β-strand	283-287	5	3
α-helix	290-300	11
β-strand	313-321	9	3
β-strand	324-332	9	3
α-helix	338-339	2
β-strand	340-342	3	3
β-strand	351-352	2	3
α-helix	353-359	7
α-helix	368-372	5

Chain B: 21 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	34-42	9	1
β-strand	47	1	2
α-helix	60-62	3
β-strand	70	1	2
α-helix	72-88	17
α-helix	96-97	2
β-strand	102-106	5	1
α-helix	110-123	14
α-helix	128-130	3
β-strand	144-145	2	1
α-helix	162-173	12
α-helix	175-181	7
α-helix	186-195	10
α-helix	202-205	4
α-helix	206-210	5
α-helix	211-218	8
α-helix	221-224	4
α-helix	229-247	19
α-helix	252-255	4
α-helix	256-260	5
α-helix	261-276	16
β-strand	283-287	5	1
α-helix	290-300	11
β-strand	313-321	9	1
β-strand	324-332	9	1
α-helix	338-339	2
β-strand	340-341	2	1
β-strand	351-352	2	1
α-helix	353-360	8
α-helix	361-363	3
α-helix	368-372	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prostatic acid phosphatase	A, B	protein	347	Homo sapiens	P15309 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8XJ4_1 Prostatic acid phosphatase (chains A, B)
LAKELKFVTLVFRHGDRSPIDTFPTDPIKESSWPQGFGQLTQLGMEQHYELGEYIRKRYR
KFLNESYKHEQVYIRSTDVDRTLMSAMTNLAALFPPEGVSIWNPILLWQPIPVHTVPLSE
DQLLYLPFRNCPRFQELESETLKSEEFQKRLHPYKDFIATLGKLSGLHGQDLFGIWSKVY
DPLYCESVHNFTLPSWATEDTMTKLRELSELSLLSLYGIHKQKEKSRLQGGVLVNEILNH
MKRATQIPSYKKLIMYSAHDTTVSGLQMALDVYNGLLPPYASCHLTELYFEKGEYFVEMY
YRNETQHEPYPLMLPGCSPSCPLERFAELVGPVIPQDWSTECMTTNS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
MAN	alpha-D-mannopyranose	C6 H12 O6	1

Primary citation

Purification, identification and Cryo-EM structure of prostatic acid phosphatase in human semen. Liu, X., Yu, L., Xia, Z. et al. Biochem Biophys Res Commun (2024) 702:149652-149652. DOI 10.1016/j.bbrc.2024.149652 · PubMed

Other PDB entries of the same protein (UniProt P15309 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3PPD 1.5 Å, GGVLVN segment from Human Prostatic Acid Phosphatase Residues 260-265, involved in…
9NMV 1.97 Å, TCR156 S32Halpha bound to HLA A*02:01-PAP
9NMY 2.01 Å, TCR156 S32Qalpha bound to HLA A*02:01-PAP
9NMU 2.1 Å, TCR156 bound to HLA A*02:01-PAP
9NMW 2.11 Å, TCR156 S30Ealpha S32Qalpha bound to HLA A*02:01-PAP
9NMX 2.19 Å, TCR156 S32Malpha variant bound to HLA A*02:01-PAP
1ND6 2.4 Å, Crystal Structures of Human Prostatic Acid Phosphatase in Complex with a Phosphate Ion…
9YTD 2.5 Å, Designed antibody vAB66 targeting PAP-HLA A*02:01
1ND5 2.9 Å, Crystal Structures of Human Prostatic Acid Phosphatase in Complex with a Phosphate Ion…
2HPA 2.9 Å, Structural origins of L(+)-tartrate inhibition of human prostatic acid phosphatase
1CVI 3.2 Å, Crystal structure of human prostatic acid phosphatase
2L3H NMR Structure in a Membrane Environment Reveals Putative Amyloidogenic Regions of the…

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