8W90: CD4-D1D2 with Nb457

crystal structure of CD4-D1D2 with Nb457. Determined by X-ray diffraction at 1.81 Å resolution. Released 4 Sept 2024.

Method: X-ray diffraction
Resolution: 1.81 Å
Organisms: Vicugna pacos, Homo sapiens
Chains: 6
Atoms: 6,936
Mol. weight: 102.93 kDa
Released: 4 Sept 2024

Explore 8W90 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8W90 contains 15 α-helices and 93 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: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	18-24	7	1
β-strand	34-39	6	2
β-strand	46-51	6	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	69-73	5	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-98	7	2
β-strand	113-114	2	2
β-strand	118-123	6	2

Chains B and D: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	3
β-strand	12-14	3	4
β-strand	17	1	5
β-strand	26-30	5	3
β-strand	35-38	4	3
β-strand	41-42	2	3
β-strand	55-56	2	4
α-helix	59-64	6
β-strand	66	1	5
β-strand	69-71	3	4
α-helix	76-78	3
β-strand	80-86	7	3
β-strand	89-98	10	3
β-strand	99-102	4	6
β-strand	108-109	2	7
β-strand	114-119	6	6
β-strand	127-131	5	8
β-strand	137-140	4	8
β-strand	143-146	4	6
α-helix	151-153	3
β-strand	155-163	9	8
β-strand	166-174	9	8
β-strand	176-177	2	7

Chain C: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-13	4	10
β-strand	18-25	8	9
β-strand	34-39	6	10
β-strand	46-51	6	10
β-strand	58-60	3	10
α-helix	62-64	3
β-strand	69-73	5	9
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-98	7	10
β-strand	113-114	2	10
β-strand	118-123	6	10

Chain E: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	17
β-strand	11-13	3	18
β-strand	18-25	8	17
α-helix	29-31	3
β-strand	34-39	6	19
β-strand	46-51	6	19
β-strand	58-60	3	19
α-helix	62-64	3
β-strand	69-73	5	17
β-strand	78-83	6	17
α-helix	88-90	3
β-strand	92-98	7	19
β-strand	113-114	2	19
β-strand	118-120	3	19
β-strand	121-123	3	18

Chain F: 2 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	20
β-strand	12-14	3	21
β-strand	17	1	22
β-strand	26-30	5	20
β-strand	35-38	4	20
β-strand	55-56	2	21
α-helix	59-62	4
β-strand	66	1	22
β-strand	69-71	3	21
α-helix	76-78	3
β-strand	80-86	7	20
β-strand	89-98	10	20
β-strand	99-102	4	23
β-strand	107-108	2	24
β-strand	114-119	6	23
β-strand	127-131	5	25
β-strand	137-139	3	25
β-strand	143-146	4	23
β-strand	155-163	9	25
β-strand	166-174	9	25
β-strand	175-176	2	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NB457	A, C, E	protein	134	Vicugna pacos
T-cell surface glycoprotein CD4	B, D, F	protein	178	Homo sapiens	P01730 (AlphaFold model)

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

>8W90_1 NB457 (chains A, C, E)
MGEVQLVESGGGLVQAGGSLRLSCAASGRTISSVAMGWFRQAPEKEREFVAAITWSGDYT
NVADSMKGRFTISRDNARKTVSLQLTNLKPEDTAVYYCAADLRGGSIYGTADYVYWGQGT
QVTVSSLEHHHHHH

Sequence of entity 2 (B, D, F), FASTA

>8W90_2 T-cell surface glycoprotein CD4 (chains B, D, F)
KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRS
LWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLES
PPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLA

Primary citation

Structure of CD4-D1D2 domain and nanobody Nb457 at 1.78 Angstroms resolution. Wang, X.Y., Wang, Y.X. To be published.

Other PDB entries of the same protein (UniProt P01730 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4H8W 1.85 Å, Crystal structure of non-neutralizing and ADCC-potent antibody N5-i5 in complex with…
2NY1 1.99 Å, HIV-1 gp120 Envelope Glycoprotein (I109C, T257S, S334A, S375W, Q428C) Complexed with CD4…
1CDY 2.0 Å, Structure of T-cell surface glycoprotein CD4 mutant with gly 47 replaced by ser
2NXY 2.0 Å, HIV-1 gp120 Envelope Glycoprotein(S334A) Complexed with CD4 and Antibody 17b
2NY2 2.0 Å, HIV-1 gp120 Envelope Glycoprotein (T123C, T257S, S334A, S375W, G431C) Complexed with CD4…
2NY3 2.0 Å, HIV-1 gp120 Envelope Glycoprotein (K231C, T257S, E267C, S334A, S375W) Complexed with CD4…
2NY4 2.0 Å, HIV-1 gp120 Envelope Glycoprotein (K231C, T257S, E268C, S334A, S375W) Complexed with CD4…
2NXZ 2.04 Å, HIV-1 gp120 Envelope Glycoprotein (T257S, S334A, S375W) Complexed with CD4 and Antibody…
3S5L 2.1 Å, Crystal structure of CD4 mutant bound to HLA-DR1
3O2D 2.19 Å, Crystal structure of HIV-1 primary receptor CD4 in complex with a potent antiviral…
1G9M 2.2 Å, HIV-1 HXBC2 GP120 envelope glycoprotein complexed with CD4 and induced neutralizing…
1RZJ 2.2 Å, HIV-1 HXBC2 GP120 envelope glycoprotein complexed with CD4 and induced neutralizing…

Browse structure collections

About this viewer

MolViewer shows 8W90 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.