5G2E: Nap1 H2A H2B complex

Structure of the Nap1 H2A H2B complex. Determined by X-ray diffraction at 6.7 Å resolution. Released 3 Aug 2016.

Method: X-ray diffraction
Resolution: 6.7 Å
Organisms: SACCHAROMYCES CEREVISIAE, XENOPUS LAEVIS
Chains: 24
Atoms: 32,814
Mol. weight: 571.42 kDa
Released: 3 Aug 2016

Explore 5G2E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5G2E contains 222 α-helices and 96 β-strands across 24 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.

Chains A, E, I, M, Q and U: 13 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	83-86	4
α-helix	90-139	50
α-helix	144-146	3
α-helix	147-159	13
α-helix	166-168	3
α-helix	188-193	6
α-helix	197-200	4
α-helix	205-211	7
β-strand	214-221	8	1
β-strand	228-235	8	1
β-strand	243	1	2
β-strand	247-254	8	1
β-strand	266-271	6	1
β-strand	276	1	2
α-helix	312-316	5
α-helix	318-320	3
α-helix	333-347	15
α-helix	348-352	5
α-helix	356-361	6

Chains B, F, J, N, R and V: 15 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	90-140	51
α-helix	144-146	3
α-helix	147-159	13
α-helix	163-165	3
α-helix	188-193	6
α-helix	197-200	4
α-helix	205-210	6
α-helix	211-213	3
β-strand	214-222	9	3
β-strand	228-235	8	3
β-strand	243	1	4
β-strand	247-254	8	3
β-strand	266-271	6	3
β-strand	276	1	4
α-helix	279-281	3
α-helix	312-316	5
α-helix	318-320	3
α-helix	330-333	4
α-helix	336-347	12
α-helix	348-352	5
α-helix	356-361	6

Chain C: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
α-helix	27-36	10
β-strand	42-43	2	5
α-helix	46-72	27
β-strand	77-78	2	6
α-helix	80-89	10
α-helix	91-96	6

Chains D, H, L, P, T and X: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	6
α-helix	53-80	28
β-strand	85-86	2	5
α-helix	88-98	11
α-helix	101-120	20

Chain G: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
α-helix	27-36	10
β-strand	42-43	2	11
α-helix	46-72	27
β-strand	77-78	2	12
α-helix	80-89	10
α-helix	91-98	8

Chains K and S: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
α-helix	27-36	10
β-strand	42-43	2	17
α-helix	46-72	27
β-strand	77-78	2	18
α-helix	80-89	10
α-helix	93-101	9

Chain O: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
α-helix	27-36	10
β-strand	42-43	2	23
α-helix	46-72	27
β-strand	77-78	2	24
α-helix	80-89	10
α-helix	91-99	9

Chain W: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
α-helix	27-36	10
β-strand	42-43	2	35
α-helix	46-72	27
β-strand	77-78	2	36
α-helix	80-89	10
α-helix	91-100	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nucleosome assembly protein	A, B, E, F, I, J, M, N, Q, R, U, V	protein	310	SACCHAROMYCES CEREVISIAE	P25293 (AlphaFold model)
Histone H2A type 1	C, G, K, O, S, W	protein	107	XENOPUS LAEVIS	P06897 (AlphaFold model)
Histone H2B 1.1	D, H, L, P, T, X	protein	100	XENOPUS LAEVIS	P02281 (AlphaFold model)

Sequence of entity 1 (A, B, E, F, I, J, M, N, Q, R, U, V), FASTA

>5G2E_1 NUCLEOSOME ASSEMBLY PROTEIN (chains A, B, E, F, I, J, M, N, Q, R, U, V)
SQDPENLYFQGLGSLVGQDSGYVGGLPKNVKEKLLSLKTLQSELFEVEKEFQVEMFELEN
KFLQKYKPIWEQRSRIISGQEQPKPEQIAKGQEIVESLNETELLVDEEEKAQNDSEEEQV
KGIPSFWLTALENLPIVCDTITDRDAEVLEYLQDIGLEYLTDGRPGFKLLFRFDSSANPF
FTNDILCKTYFYQKELGYSGDFIYDHAEGCEISWKDNAHNVTVDLEMRKQRNKTTKQVRT
IEKITPIESFFNFFDPPKIQNEDQDEELEEDLEERLALDYSIGEQLKDKLIPRAVDWFTG
AALEFEFEED

Sequence of entity 2 (C, G, K, O, S, W), FASTA

>5G2E_2 HISTONE H2A TYPE 1 (chains C, G, K, O, S, W)
MKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAAR
DNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPK

Sequence of entity 3 (D, H, L, P, T, X), FASTA

>5G2E_3 HISTONE H2B 1.1 (chains D, H, L, P, T, X)
MKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNK
RSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Primary citation

Structural Evidence for Nap1-Dependent H2A-H2B Deposition and Nucleosome Assembly. Aguilar-Gurrieri, C., Larabi, A., Vinayachandran, V. et al. EMBO J (2016) 35:1465. DOI 10.15252/EMBJ.201694105 · PubMed

Other PDB entries of the same protein (UniProt P25293 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9B3I 2.88 Å, Cryo-EM structure of yeast (Nap1)2-H2A-H2B-Kap114-RanGTP
2AYU 3.0 Å, The structure of nucleosome assembly protein suggests a mechanism for histone binding…
2Z2R 3.2 Å, Nucleosome assembly proteins I (NAP-1, 74-365)
9B23 3.2 Å, Cryo-EM structure of Nap1 core
9B31 3.2 Å, Cryo-EM structure of yeast (Nap1)2-Kap114-H2A-H2B
9B3F 3.54 Å, Cryo-EM structure of yeast (Nap1)2-H2A-H2B-Kap114

Browse structure collections

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