2XJZ: LMO2:LDB1-LID complex, C2 crystal form

Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form. Determined by X-ray diffraction at 2.8 Å resolution. Released 21 Jul 2010.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: HOMO SAPIENS
Chains: 10
Atoms: 6,166
Mol. weight: 98.18 kDa
Ligands: ZN
Released: 21 Jul 2010

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

Secondary structure: helices and β-sheets

2XJZ contains 39 α-helices and 90 β-strands across 10 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: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	34-38	5	1
β-strand	41-43	3	1
β-strand	49	1	2
β-strand	56	1	2
β-strand	63-67	5	3
β-strand	70-72	3	3
α-helix	74-81	8
α-helix	82-84	3
β-strand	85-86	2	4
β-strand	93-94	2	4
β-strand	99-103	5	5
β-strand	106-109	4	5
α-helix	110-112	3
β-strand	114	1	6
α-helix	120	1
β-strand	121	1	6
α-helix	122	1
β-strand	127-131	5	7
β-strand	134-137	4	7
α-helix	138-140	3
α-helix	141-147	7

Chain B: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	34-38	5	8
β-strand	41-43	3	8
β-strand	49	1	9
β-strand	56	1	9
β-strand	64-67	4	10
β-strand	70-72	3	10
α-helix	74-81	8
α-helix	82-84	3
β-strand	85-86	2	11
β-strand	93-94	2	11
β-strand	99-103	5	12
β-strand	106-109	4	12
α-helix	110-112	3
β-strand	114	1	13
α-helix	120	1
β-strand	121	1	13
α-helix	122	1
β-strand	127-131	5	14
β-strand	134-137	4	14
α-helix	138-140	3
α-helix	141-147	7

Chain C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	49	1	15
β-strand	56	1	15
β-strand	65-67	3	16
β-strand	70-72	3	16
α-helix	74-81	8
β-strand	85-86	2	17
β-strand	93-94	2	17
β-strand	99-103	5	18
β-strand	106-109	4	18
α-helix	110-112	3
β-strand	114	1	19
β-strand	121	1	19
β-strand	127-131	5	20
β-strand	134-137	4	20
α-helix	141-147	7

Chain D: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	20-21	2
β-strand	22	1	21
β-strand	23	1	22
β-strand	29	1	21
β-strand	34-38	5	22
β-strand	41-44	4	22
β-strand	49	1	23
β-strand	56	1	23
β-strand	63-67	5	24
β-strand	70-72	3	24
α-helix	74-81	8
α-helix	82-84	3
β-strand	85-86	2	25
β-strand	93-94	2	25
β-strand	99-103	5	26
β-strand	106-109	4	26
α-helix	110-112	3
β-strand	114	1	27
α-helix	120	1
β-strand	121	1	27
α-helix	122	1
β-strand	127-131	5	28
β-strand	134-137	4	28
α-helix	138-140	3
α-helix	141-146	6

Chain E: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	36-38	3	29
β-strand	41-43	3	29
β-strand	49	1	30
β-strand	56	1	30
β-strand	63-67	5	31
β-strand	70-72	3	31
α-helix	74-81	8
α-helix	82-84	3
β-strand	85-86	2	32
β-strand	93-94	2	32
β-strand	99-103	5	33
β-strand	106-109	4	33
α-helix	110-112	3
β-strand	114	1	34
α-helix	120	1
β-strand	121	1	34
α-helix	122	1
β-strand	127-131	5	35
β-strand	134-137	4	35
α-helix	138-140	3
α-helix	142-145	4

Chain I: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	337-339	3	7
β-strand	344-345	2	5
α-helix	346-348	3
β-strand	355-357	3	3
α-helix	358	1
β-strand	359-362	4	1

Chain J: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	336-339	4	14
β-strand	344-345	2	12
α-helix	346-349	4
β-strand	355-356	2	10
β-strand	359-362	4	8

Chain K: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	337-339	3	20
β-strand	344-345	2	18
α-helix	346-349	4
β-strand	355	1	16

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rhombotin-2	A, B, C, D, E	protein	131	HOMO SAPIENS	P25791 (AlphaFold model)
Lim domain-binding protein 1	I, J, K, L, M	protein	36	HOMO SAPIENS	Q86U70 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E), FASTA

>2XJZ_1 RHOMBOTIN-2 (chains A, B, C, D, E)
SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL
RLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCE
QDIYEWTKING

Sequence of entity 2 (I, J, K, L, M), FASTA

>2XJZ_2 LIM DOMAIN-BINDING PROTEIN 1 (chains I, J, K, L, M)
SVPDVMVVGEPTLMGGEFGDEDERLITRLENTQFDA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	20

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

Primary citation

Structure of the Leukemia Oncogene Lmo2: Implications for the Assembly of a Hematopoietic Transcription Factor Complex. El Omari, K., Hoosdally, S.J., Tuladhar, K. et al. Blood (2011) 117:2146. DOI 10.1182/BLOOD-2010-07-293357 · PubMed

Other PDB entries of the same protein (UniProt P25791 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2XJY 2.4 Å, Crystal structure of the LMO2:LDB1-LID complex, P21 crystal form
2YPA 2.8 Å, Structure of the SCL:E47:LMO2:LDB1 complex bound to DNA
4KFZ 2.8 Å, Crystal structure of LMO2 and anti-LMO2 VH complex

Browse structure collections

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