2V4H: NEMO CC2-LZ domain - 1D5 DARPin complex

NEMO CC2-LZ domain - 1D5 DARPin complex. Determined by X-ray diffraction at 2.9 Å resolution. Released 3 Nov 2009.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: MUS MUSCULUS, SYNTHETIC CONSTRUCT
Chains: 4
Atoms: 3,542
Mol. weight: 55.64 kDa
Released: 3 Nov 2009

Explore 2V4H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2V4H contains 20 α-helices and 2 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: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	252-288	37
α-helix	290-333	44

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	249-288	40
α-helix	290-335	46

Chain C: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	14-24	11
α-helix	27-35	9
α-helix	50-56	7
α-helix	60-67	8
α-helix	83-89	7
α-helix	93-101	9
β-strand	109	1	1
β-strand	115	1	1
α-helix	116-123	8
α-helix	126-130	5

Chain D: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	14-24	11
α-helix	27-35	9
α-helix	50-56	7
α-helix	60-68	9
α-helix	83-90	8
α-helix	93-101	9
α-helix	116-123	8
α-helix	126-133	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nf-kappa-B essential modulator	A, B	protein	110	MUS MUSCULUS	O88522 (AlphaFold model)
1D5 darpin	C, D	protein	136	SYNTHETIC CONSTRUCT

Sequence of entity 1 (A, B), FASTA

>2V4H_1 NF-KAPPA-B ESSENTIAL MODULATOR (chains A, B)
MGSSHHHHHHSSGLVPRGSHMASMQLEDLRQQLQQAEEALVAKQELIDKLKEEAEQHKIV
METVPVLKAQADIYKADFQAERHAREKLVEKKEYLQEQLEQLQREFNKLK

Sequence of entity 2 (C, D), FASTA

>2V4H_2 1D5 DARPIN (chains C, D)
HHHHHHHHHHGSDLGKKLLEAARAGQDDEVRILMANGADVNANDRKGNTPLHLAADYDHL
EIVEVLLKHGADVNAHDNDGSTPLHLAALFGHLEIVEVLLKHGADVNAQDKFGKTAFDIS
IDNGNEDLAEILQKLN

Primary citation

Darpin-Assisted Crystallography of the Cc2-Lz Domain of Nemo Reveals a Coupling between Dimerization and Ubiquitin-Binding. Grubisha, O., Kaminska, M., Duquerroy, S. et al. J Mol Biol (2010) 395:89. DOI 10.1016/J.JMB.2009.10.018 · PubMed

Other PDB entries of the same protein (UniProt O88522 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4OWF 2.0 Å, Crystal structure of the NEMO CoZi in complex with HOIP NZF1 domain
3JSV 2.7 Å, Crystal structure of mouse NEMO CoZi in complex with Lys63-linked di-ubiquitin
3F89 2.8 Å, NEMO CoZi domain
2ZVO 2.9 Å, NEMO CoZi domain in complex with diubiquitin in C2 space group
2ZVN 3.0 Å, NEMO CoZi domain incomplex with diubiquitin in P212121 space group

Browse structure collections

About this viewer

MolViewer shows 2V4H directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.