4HC1: Loop deleted mutant of human MAdCAM-1 D1D2

Crystal structure of a loop deleted mutant of human MAdCAM-1 D1D2 complexed with Fab 10G3. Determined by X-ray diffraction at 2.87 Å resolution. Released 23 Jan 2013.

Method: X-ray diffraction
Resolution: 2.87 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 9,648
Mol. weight: 138.36 kDa
Ligands: NAG
Released: 23 Jan 2013

Explore 4HC1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4HC1 contains 34 α-helices and 128 β-strands across 6 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: 1 helix, 20 β-strands

Element	Residues	Length	Sheet
β-strand	12-16	5	1
β-strand	21-26	6	2
β-strand	35-38	4	1
β-strand	48-50	3	2
β-strand	54-59	6	2
β-strand	68-75	8	1
β-strand	80-90	11	1
β-strand	91	1	3
β-strand	96-99	4	4
β-strand	103	1	5
β-strand	109-117	9	4
β-strand	118	1	3
β-strand	125-131	7	6
β-strand	134-135	2	6
β-strand	141	1	4
β-strand	145-149	5	4
β-strand	160-168	9	4
α-helix	176-177	2
β-strand	179-188	10	6
β-strand	191-200	10	6
β-strand	201	1	5

Chain B: 1 helix, 20 β-strands

Element	Residues	Length	Sheet
β-strand	12-16	5	18
β-strand	21-26	6	19
β-strand	35-38	4	18
β-strand	48-50	3	19
β-strand	54-59	6	19
β-strand	68-75	8	18
β-strand	80-90	11	18
β-strand	91	1	20
β-strand	96-99	4	21
β-strand	103	1	22
β-strand	109-117	9	21
β-strand	118	1	20
β-strand	125-131	7	23
β-strand	134-135	2	23
β-strand	141	1	21
β-strand	145-151	7	21
β-strand	158-168	11	21
α-helix	176-177	2
β-strand	179-188	10	23
β-strand	191-200	10	23
β-strand	201	1	22

Chains H and M: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
β-strand	34-41	8	9
β-strand	45-53	9	9
β-strand	58-60	3	9
α-helix	62-64	3
β-strand	68-69	2	7
β-strand	72-73	2	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-99	8	9
β-strand	107-108	2	9
β-strand	112-114	3	9
β-strand	115-116	2	8
α-helix	119-121	3
β-strand	122	1	10
α-helix	123-124	2
β-strand	125-129	5	11
α-helix	130-132	3
β-strand	140-150	11	11
β-strand	151	1	10
β-strand	156-159	4	12
α-helix	160-162	3
β-strand	168-170	3	11
α-helix	171-173	3
β-strand	174-176	3	11
β-strand	179-189	11	11
β-strand	199-204	6	12
α-helix	205-207	3
β-strand	209-214	6	12
α-helix	215	1

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-25	7	13
β-strand	33-38	6	14
β-strand	44-49	6	14
β-strand	53-54	2	14
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	85-90	6	14
α-helix	96	1
β-strand	97-98	2	14
β-strand	102-107	6	14
β-strand	111	1	15
β-strand	114-118	5	16
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	16
β-strand	140	1	15
β-strand	145-150	6	17
β-strand	153-155	3	17
β-strand	159-163	5	16
α-helix	164-167	4
β-strand	173-182	10	16
α-helix	183-186	4
β-strand	191-197	7	17
α-helix	204	1
β-strand	205-210	6	17

Chain N: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	30
β-strand	10-13	4	31
β-strand	18-25	8	30
β-strand	33-38	6	31
β-strand	44-49	6	31
β-strand	53-54	2	31
β-strand	62-67	6	30
β-strand	70-76	7	30
α-helix	80-82	3
β-strand	85-90	6	31
α-helix	96	1
β-strand	97-98	2	31
β-strand	102-106	5	31
β-strand	111	1	32
β-strand	114-118	5	33
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	33
β-strand	140	1	32
β-strand	145-150	6	34
β-strand	153-155	3	34
β-strand	159-163	5	33
α-helix	164-167	4
β-strand	173-182	10	33
α-helix	183-186	4
β-strand	191-197	7	34
α-helix	204	1
β-strand	205-210	6	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mucosal addressin cell adhesion molecule 1	A, B	protein	206	Homo sapiens	Q13477 (AlphaFold model)
10G3 heavy chain	H, M	protein	220	Mus musculus
10G3 light chain	L, N	protein	214	Mus musculus

Sequence of entity 1 (A, B), FASTA

>4HC1_1 Mucosal addressin cell adhesion molecule 1 (chains A, B)
VKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAVQSDTGRSVLTVR
NASLSAAGTRVCVGSCGGRTFQHTVQLLVYAFPNQLTVSPAALVPGDPEVACTAHKVTPV
DPNALSFSLLVGGQELEGAQALGPEVQQEPIGGDVLFRVTERWRLPPLGTPVPPALYCQA
TMRLPGLELSHRQAIPVLGGENLYFQ

Sequence of entity 2 (H, M), FASTA

>4HC1_2 10G3 heavy chain (chains H, M)
DVQLQESGPGLVKPSQSLSLTCSVTGYSITSGYYWNWIRQFPGNKLEWMGYISYDGSNNY
NPSLKNRVSITRDTSKNHFFLKLSSVTTEDTATYYCARASDSDGFAYWGQGTLVTVSAAK
TTAPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAILQSGLY
TLSSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIEPRVP

Sequence of entity 3 (L, N), FASTA

>4HC1_3 10G3 light chain (chains L, N)
DILMTQSPSSMSVSLGDTVSFTCHASQGIGRNIGWLQQKPGKSFKGLIYHGTNLKDGVPS
RFSGSGSGADYSLTISRIESEDFADYYCIQYVQFPYTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

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

Primary citation

A Different Fold with an Integrin-Binding Loop Specialized for Flexibility in Mucosal Addressin Cell Adhesion Molecule-1. Springer, T., Yu, Y., Zhu, J. et al. To be published.

Other PDB entries of the same protein (UniProt Q13477 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HBQ 1.4 Å, Crystal structure of a loop deleted mutant of Human MAdCAM-1 D1D2
4HD9 1.7 Å, Crystal structure of native human MAdCAM-1 D1D2 domain
1GSM 1.9 Å, A reassessment of the MAdCAM-1 structure and its role in integrin recognition.
1BQS 2.2 Å, The crystal structure of mucosal addressin cell adhesion molecule-1 (madcam-1)
4HCR 2.3 Å, Crystal structure of human MAdCAM-1 D1D2 complexed with Fab PF-547659
9P95 3.05 Å, CryoEM structure of integrin alpha4beta7 bound to MAdCAM-1

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