3O2D: HIV-1 primary receptor CD4

Crystal structure of HIV-1 primary receptor CD4 in complex with a potent antiviral antibody. Determined by X-ray diffraction at 2.19 Å resolution. Released 22 Dec 2010.

Method: X-ray diffraction
Resolution: 2.19 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 4,966
Mol. weight: 69.58 kDa
Released: 22 Dec 2010

Explore 3O2D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3O2D contains 23 α-helices and 68 β-strands across 3 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: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	13
β-strand	12-14	3	14
β-strand	17	1	15
β-strand	26-30	5	13
β-strand	35-40	6	13
β-strand	43-46	4	13
α-helix	52-54	3
β-strand	55-56	2	14
α-helix	59-64	6
β-strand	66	1	15
β-strand	69-71	3	14
α-helix	76-78	3
β-strand	80-86	7	13
β-strand	89-98	10	13
β-strand	99-102	4	16
β-strand	107-109	3	17
β-strand	114-119	6	16
β-strand	127-131	5	18
β-strand	137-140	4	18
β-strand	143-146	4	16
α-helix	151-153	3
β-strand	155-163	9	18
β-strand	166-174	9	18
β-strand	175-177	3	17

Chain H: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
α-helix	7-9	3
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	46-52	7	8
β-strand	56-59	4	8
α-helix	61-63	3
β-strand	64	1	7
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-95	8	8
β-strand	100E-103	4	8
β-strand	107-111	5	8
α-helix	115-116	2
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	159	1	11
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-185	10	10
α-helix	186-188	3
β-strand	189	1	12
β-strand	192	1	12
β-strand	194-200	7	11
α-helix	201-203	3
β-strand	205-211	7	11

Chain L: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	30-30A	2	3
β-strand	30F-31	2	3
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
β-strand	96-97	2	2
β-strand	101-106	6	2
β-strand	110	1	4
α-helix	111-112	2
β-strand	113-117	5	5
α-helix	118-120	3
α-helix	121-126	6
β-strand	128-138	11	5
β-strand	139	1	4
β-strand	144-149	6	6
β-strand	152-153	2	6
α-helix	154	1
β-strand	158-162	5	5
α-helix	163-166	4
β-strand	172-181	10	5
α-helix	182-186	5
β-strand	190-196	7	6
β-strand	204-209	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ibalizumab light chain	L	protein	219	Mus musculus
ibalizumab heavy chain	H	protein	225	Mus musculus
T-cell surface glycoprotein CD4	A	protein	188	Homo sapiens	P01730 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>3O2D_1 ibalizumab light chain (chains L)
DIVMTQSPDSLAVSLGERVTMNCKSSQSLLYSTNQKNYLAWYQQKPGQSPKLLIYWASTR
ESGVPDRFSGSGSGTDFTLTISSVQAEDVAVYYCQQYYSYRTFGGGTKLEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (H), FASTA

>3O2D_2 ibalizumab heavy chain (chains H)
QVQLQQSGPEVVKPGASVKMSCKASGYTFTSYVIHWVRQKPGQGLDWIGYINPYNDGTDY
DEKFKGKATLTSDTSTSTAYMELSSLRSEDTAVYYCAREKDNYATGAWFAYWGQGTLVTV
SSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKYG

Sequence of entity 3 (A), FASTA

>3O2D_3 T-cell surface glycoprotein CD4 (chains A)
KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRS
LWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLES
PPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAFQ
KAHHHHHH

Primary citation

Crystal Structure of HIV-1 Primary Receptor CD4 in Complex with a Potent Antiviral Antibody. Freeman, M.M., Seaman, M.S., Rits-Volloch, S. et al. Structure (2010) 18:1632-1641. DOI 10.1016/j.str.2010.09.017 · PubMed

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

8W90 1.81 Å, crystal structure of CD4-D1D2 with Nb457
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
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…

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