5CL1: Maltose-binding periplasmic protein,Norrin

Complex structure of Norrin with human Frizzled 4. Determined by X-ray diffraction at 3.8 Å resolution. Released 12 Aug 2015.

Method: X-ray diffraction
Resolution: 3.8 Å
Organisms: Escherichia coli O157:H7, Homo sapiens
Chains: 4
Atoms: 9,227
Mol. weight: 138.41 kDa
Ligands: NAG
Released: 12 Aug 2015

Explore 5CL1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5CL1 contains 65 α-helices and 90 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: 27 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	1
α-helix	17-30	14
β-strand	35-38	4	1
α-helix	43-53	11
β-strand	59-63	5	1
α-helix	64-73	10
β-strand	76	1	2
α-helix	77-79	3
α-helix	83-88	6
β-strand	89	1	3
α-helix	91-95	5
β-strand	98-99	2	4
β-strand	102-103	2	4
β-strand	105-107	3	1
β-strand	109-110	2	5
β-strand	111	1	6
β-strand	114-118	5	7
β-strand	128	1	8
α-helix	132-140	9
β-strand	145-147	3	7
α-helix	154-161	8
α-helix	162-164	3
β-strand	167	1	9
β-strand	170-171	2	10
β-strand	176-177	2	10
β-strand	182	1	9
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	7
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	7
α-helix	246-248	3
β-strand	249	1	8
β-strand	250	1	11
β-strand	253	1	11
α-helix	254-255	2
β-strand	258-259	2	12
β-strand	260	1	6
β-strand	262-266	5	1
β-strand	267	1	2
α-helix	273-278	6
α-helix	279-284	6
α-helix	287-296	10
β-strand	301-302	2	5
β-strand	304	1	3
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	12
α-helix	330-331	2
α-helix	334-336	3
α-helix	337-352	16
α-helix	357-367	11
α-helix	1033-1035	3
β-strand	1040-1048	9	13
β-strand	1058-1067	10	13
α-helix	1072	1
β-strand	1073-1077	5	14
α-helix	1078	1
β-strand	1079-1080	2	15
β-strand	1081	1	16
β-strand	1084	1	16
β-strand	1089-1092	4	14
β-strand	1094-1104	11	17
β-strand	1107	1	18
β-strand	1117	1	18
β-strand	1119	1	19
β-strand	1120-1130	11	17

Chain B: 26 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	20
α-helix	17-30	14
β-strand	35-38	4	20
α-helix	43-53	11
β-strand	59-63	5	20
α-helix	64-73	10
β-strand	76	1	21
α-helix	77-79	3
α-helix	83-88	6
β-strand	89	1	22
α-helix	91-95	5
β-strand	98-99	2	23
β-strand	102-103	2	23
β-strand	105-107	3	20
β-strand	109-110	2	24
β-strand	111	1	25
β-strand	114-118	5	26
β-strand	128	1	27
α-helix	132-140	9
β-strand	145-147	3	26
α-helix	154-161	8
α-helix	162-164	3
β-strand	167	1	28
β-strand	170-171	2	29
β-strand	176-177	2	29
β-strand	182	1	28
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	26
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	26
α-helix	246-248	3
β-strand	249-250	2	27
β-strand	253-254	2	27
α-helix	255	1
β-strand	258-259	2	30
β-strand	260	1	25
β-strand	262-266	5	20
β-strand	267	1	21
α-helix	273-278	6
α-helix	279-284	6
α-helix	287-296	10
β-strand	301-302	2	24
β-strand	304	1	22
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	30
α-helix	330-331	2
α-helix	334-336	3
α-helix	337-352	16
α-helix	357-367	11
β-strand	1040-1048	9	14
β-strand	1058-1067	10	14
α-helix	1072	1
β-strand	1073-1077	5	13
α-helix	1078-1079	2
β-strand	1080	1	19
β-strand	1089-1092	4	13
β-strand	1094-1104	11	15
β-strand	1107-1108	2	31
β-strand	1116-1117	2	31
β-strand	1119-1130	12	15

Chain C: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	46-47	2	32
β-strand	60-61	2	32
α-helix	72-79	8
α-helix	80-82	3
α-helix	83-88	6
α-helix	94-102	9
β-strand	105	1	32
β-strand	114	1	32
β-strand	115-116	2	33
α-helix	118-134	17
α-helix	141-143	3
β-strand	158-159	2	33

Chain D: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	46-47	2	34
β-strand	60-61	2	34
α-helix	72-79	8
α-helix	80-82	3
α-helix	83-88	6
α-helix	94-102	9
β-strand	105	1	34
β-strand	114	1	34
β-strand	116	1	35
α-helix	118-134	17
α-helix	141-143	3
β-strand	159	1	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltose-binding periplasmic protein,Norrin	A, B	protein	483	Escherichia coli O157:H7, Homo sapiens	P0AEY0 (AlphaFold model), Q00604 (AlphaFold model)
Frizzled-4	C, D	protein	131	Homo sapiens	Q9ULV1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5CL1_1 Maltose-binding periplasmic protein,Norrin (chains A, B)
HHHHHHHHMAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQV
AATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAV
EALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFK
YENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPW
AWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGL
EAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINA
ASGRQTVDEALKDAQTNAAAIMDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCS
QASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEE
CNS

Sequence of entity 2 (C, D), FASTA

>5CL1_2 Frizzled-4 (chains C, D)
HHHHHHHHGDEEERRCDPIRISMCQNLGYNVTKMPNLVGHELQTDAELQLTTFTPLIQYG
CSSQLQFFLCSVYVPMCTEKINIPIGPCGGMCLSVKRRCEPVLKEFGFAWPESLNCSKFP
PQNDHNHMCME

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Structural basis of the Norrin-Frizzled 4 interaction. Shen, G., Ke, J., Wang, Z. et al. Cell Res (2015) 25:1078-1081. DOI 10.1038/cr.2015.92 · PubMed

Other PDB entries of the same protein (UniProt P0AEY0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PQP 1.07 Å, Crystal structure of maltose binding protein (Apo), mutant Trp340 to 4-Fluorotryptophan
9PQL 1.37 Å, Crystal structure of maltose binding protein (Apo), mutant Trp62 to 4-Fluorotryptophan
9PQN 1.37 Å, Crystal structure of maltose binding protein (Apo), mutant Trp340 to 4-Cyanotryptophan
9TY2 1.75 Å, Crystal structure of a Picomolar Nanobody in complex with Maltose Binding Protein, MBP,…
4WGI 1.85 Å, A Single Diastereomer of a Macrolactam Core Binds Specifically to Myeloid Cell Leukemia…
9PQK 1.87 Å, Crystal structure of maltose binding protein (Apo), mutant Trp10 to 4-Fluorotryptophan
4WVI 1.9 Å, Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB) in…
4WVJ 1.95 Å, Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB) in…
4YS9 2.0 Å, Ataxin-3 Carboxy-Terminal Region - Crystal C1 (tetragonal)
5II4 2.0 Å, Crystal structure of red abalone VERL repeat 1 with linker at 2.0 A resolution
5JON 2.04 Å, Crystal structure of the unliganded form of HCN2 CNBD
4WVG 2.05 Å, Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB).

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