3GUT: Higher-order complex of p50:RelA

Crystal structure of a higher-order complex of p50:RelA bound to the HIV-1 LTR. Determined by X-ray diffraction at 3.59 Å resolution. Released 8 Sept 2009.

Method: X-ray diffraction
Resolution: 3.59 Å
Organisms: Homo sapiens, Human immunodeficiency virus
Chains: 12
Atoms: 20,640
Mol. weight: 295.59 kDa
Released: 8 Sept 2009

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

Secondary structure: helices and β-sheets

3GUT contains 83 α-helices and 218 β-strands across 8 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: 9 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	1
α-helix	26	1
β-strand	27	1	2
α-helix	28	1
α-helix	32-34	3
α-helix	46-47	2
β-strand	48	1	2
β-strand	60-64	5	1
β-strand	71-77	7	3
α-helix	84	1
β-strand	85	1	3
α-helix	86	1
β-strand	89-91	3	4
β-strand	95-96	2	3
β-strand	99-103	5	3
β-strand	110-112	3	1
β-strand	117-119	3	4
α-helix	127-135	9
β-strand	156-157	2	5
β-strand	158-166	9	3
β-strand	172-174	3	3
β-strand	178-179	2	3
β-strand	183-184	2	5
β-strand	196-199	4	6
β-strand	203-205	3	7
β-strand	211-216	6	6
β-strand	226-230	5	7
β-strand	233-236	4	7
β-strand	238	1	6
α-helix	241-243	3
β-strand	244-245	2	6
β-strand	249-253	5	6
α-helix	255-257	3
β-strand	266-272	7	7
β-strand	273	1	8
β-strand	280	1	8
β-strand	284-289	6	7

Chain B: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	341-346	6	9
α-helix	347	1
β-strand	348	1	10
α-helix	349	1
β-strand	356	1	11
α-helix	358-360	3
β-strand	369	1	10
β-strand	381-385	5	9
β-strand	392-398	7	12
β-strand	406	1	12
β-strand	410-413	4	11
β-strand	416-417	2	12
β-strand	420-424	5	12
β-strand	431-433	3	9
β-strand	437-440	4	11
α-helix	447-460	14
α-helix	465-468	4
α-helix	471-473	3
α-helix	488-502	15
β-strand	509-519	11	12
β-strand	525-538	14	12
β-strand	550-553	4	13
β-strand	557-559	3	14
β-strand	565-570	6	13
α-helix	575-577	3
β-strand	578-585	8	14
β-strand	591-595	5	14
β-strand	597	1	13
β-strand	603-604	2	13
β-strand	608-612	5	13
α-helix	613-616	4
β-strand	625-633	9	14
β-strand	639	1	14
β-strand	643-648	6	14

Chain C: 10 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	20-25	6	15
α-helix	26-28	3
β-strand	35	1	16
β-strand	60-64	5	15
β-strand	71-77	7	17
α-helix	84	1
β-strand	85	1	17
α-helix	86	1
β-strand	89-92	4	16
β-strand	95-96	2	17
β-strand	99-103	5	17
β-strand	110-112	3	15
β-strand	116-119	4	16
α-helix	120-122	3
α-helix	126-135	10
β-strand	156-157	2	18
β-strand	158-166	9	17
β-strand	172-174	3	17
β-strand	178-179	2	17
α-helix	181-182	2
β-strand	183-184	2	18
β-strand	196-199	4	19
β-strand	203-205	3	20
β-strand	211-216	6	19
β-strand	225-229	5	20
β-strand	234-236	3	20
β-strand	238	1	19
α-helix	241-243	3
β-strand	244	1	19
α-helix	245-247	3
β-strand	249-253	5	19
α-helix	254-257	4
β-strand	266-274	9	20
β-strand	279-280	2	20
α-helix	281-283	3
β-strand	284-289	6	20

Chain D: 9 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	341-344	4	21
α-helix	347	1
β-strand	348	1	22
α-helix	349	1
β-strand	351-353	3	23
β-strand	356-357	2	24
α-helix	358-360	3
β-strand	369	1	22
β-strand	381	1	25
β-strand	382-385	4	21
β-strand	392-398	7	23
β-strand	406	1	23
β-strand	410-413	4	24
β-strand	416-417	2	23
β-strand	420-424	5	23
β-strand	433	1	25
β-strand	437-441	5	24
α-helix	447-460	14
α-helix	465-468	4
α-helix	471-473	3
α-helix	490-502	13
β-strand	509-519	11	23
β-strand	525-528	4	23
β-strand	532-539	8	23
β-strand	550-553	4	26
β-strand	557-559	3	27
β-strand	565-570	6	26
β-strand	579-585	7	27
β-strand	591-595	5	27
β-strand	597	1	26
α-helix	600-602	3
β-strand	603-604	2	26
β-strand	608-612	5	26
α-helix	613-616	4
β-strand	625-632	8	27
β-strand	639	1	27
β-strand	643-648	6	27

Chain E: 11 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	28
α-helix	26	1
β-strand	27	1	29
α-helix	28	1
α-helix	32-34	3
β-strand	48	1	29
β-strand	52	1	30
β-strand	55	1	30
β-strand	60-64	5	28
β-strand	71-77	7	31
α-helix	84	1
β-strand	85	1	31
α-helix	86	1
β-strand	89-91	3	32
β-strand	95-96	2	31
β-strand	99-103	5	31
β-strand	110-112	3	28
β-strand	117-119	3	32
α-helix	127-135	9
β-strand	156-157	2	33
β-strand	158-166	9	31
β-strand	172-174	3	31
β-strand	178-179	2	31
α-helix	181-182	2
β-strand	183-184	2	33
β-strand	196-199	4	34
β-strand	203-205	3	35
β-strand	211-216	6	34
α-helix	221-223	3
β-strand	225-230	6	35
β-strand	233-236	4	35
β-strand	238	1	34
α-helix	241-243	3
β-strand	244-245	2	34
β-strand	249-253	5	34
α-helix	255-257	3
β-strand	266-273	8	35
α-helix	275-277	3
β-strand	280	1	35
β-strand	284-289	6	35

Chain F: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	342-346	5	36
α-helix	347	1
β-strand	348	1	37
α-helix	349	1
β-strand	356	1	38
α-helix	358-360	3
β-strand	369	1	37
β-strand	381-384	4	36
β-strand	392-398	7	39
β-strand	406	1	39
β-strand	410-413	4	38
β-strand	416-417	2	39
β-strand	420-424	5	39
β-strand	431-433	3	36
β-strand	437-440	4	38
α-helix	444-446	3
α-helix	447-461	15
α-helix	465-468	4
α-helix	471-473	3
α-helix	488-501	14
α-helix	502-504	3
β-strand	509-519	11	39
β-strand	525-528	4	39
β-strand	532-538	7	39
β-strand	550-553	4	40
β-strand	557-559	3	41
β-strand	565-570	6	40
α-helix	575-577	3
β-strand	578-585	8	41
β-strand	591-595	5	41
β-strand	603-604	2	40
β-strand	608-612	5	40
α-helix	613-616	4
β-strand	625-633	9	41
β-strand	639	1	41
β-strand	643-648	6	41

Chain G: 13 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	20-25	6	42
α-helix	26-28	3
α-helix	32-34	3
β-strand	35	1	43
β-strand	60-64	5	42
β-strand	71-77	7	44
α-helix	84	1
β-strand	85	1	44
α-helix	86	1
β-strand	89-90	2	43
β-strand	95-96	2	44
β-strand	99-103	5	44
β-strand	110-112	3	42
β-strand	118-119	2	43
α-helix	120-122	3
α-helix	123-125	3
α-helix	126-135	10
β-strand	156-157	2	45
β-strand	158-166	9	44
β-strand	172-174	3	44
β-strand	178-179	2	44
α-helix	181-182	2
β-strand	183-184	2	45
β-strand	196-199	4	46
β-strand	203-205	3	47
β-strand	211-216	6	46
β-strand	225-230	6	47
β-strand	233-236	4	47
β-strand	238	1	46
α-helix	241-243	3
β-strand	244	1	46
α-helix	245-247	3
β-strand	249-253	5	46
α-helix	254-257	4
β-strand	266-274	9	47
α-helix	275-277	3
β-strand	279-280	2	47
α-helix	281-283	3
β-strand	284-289	6	47

Chain H: 11 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	341-344	4	48
α-helix	347	1
β-strand	348	1	49
α-helix	349	1
β-strand	351-353	3	50
β-strand	356	1	51
α-helix	358-360	3
β-strand	369	1	49
β-strand	381	1	52
β-strand	382-385	4	48
β-strand	392-398	7	50
β-strand	406	1	50
β-strand	410-413	4	51
β-strand	416-417	2	50
β-strand	420-424	5	50
β-strand	433	1	52
β-strand	437-440	4	51
α-helix	447-460	14
α-helix	465-468	4
α-helix	471-473	3
α-helix	488-501	14
α-helix	502-504	3
β-strand	509-519	11	50
β-strand	525-528	4	50
β-strand	532-539	8	50
α-helix	543-545	3
β-strand	550-553	4	53
β-strand	557-559	3	54
β-strand	565-566	2	55
β-strand	568-570	3	53
β-strand	580-585	6	54
β-strand	591-595	5	54
β-strand	597	1	55
α-helix	600-602	3
β-strand	603-604	2	53
β-strand	608-609	2	53
β-strand	611-612	2	55
α-helix	613-616	4
β-strand	625-631	7	54
β-strand	632	1	56
β-strand	639	1	56
β-strand	643-648	6	54

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription factor p65	A, C, E, G	protein	273	Homo sapiens	Q04206 (AlphaFold model)
Nuclear factor NF-kappa-B p105 subunit	B, D, F, H	protein	312	Homo sapiens	P19838 (AlphaFold model)
HIV-LTR Core Forward Strand	I, X	DNA	26	Human immunodeficiency virus
HIV-LTR Core Reverse Strand	J, Y	DNA	26	Human immunodeficiency virus

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

>3GUT_1 Transcription factor p65 (chains A, C, E, G)
AYVEIIEQPKQRGMRFRYKCEGRSAGSIPGERSTDTTKTHPTIKINGYTGPGTVRISLVT
KDPPHRPHPHELVGKDCRDGYYEADLCPDRSIHSFQNLGIQCVKKRDLEQAISQRIQTNN
NPFHVPIEEQRGDYDLNAVRLCFQVTVRDPAGRPLLLTPVLSHPIFDNRAPNTAELKICR
VNRNSGSCLGGDEIFLLCDKVQKEDIEVYFTGPGWEARGSFSQADVHRQVAIVFRTPPYA
DPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPD

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

>3GUT_2 Nuclear factor NF-kappa-B p105 subunit (chains B, D, F, H)
GPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLV
TNGKNIHLHAHSLVGKHCEDGVCTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEA
CIRGYNPGLLVHSDLAYLQAEGGGDRQLTDREKEIIRQAAVQQTKEMDLSVVRLMFTAFL
PDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDI
QIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDVNITKPASVFVQLRRKSDLE
TSEPKPFLYYPE

Sequence of entity 3 (I, X), FASTA

>3GUT_3 HIV-LTR Core Forward Strand (chains I, X)
AGGGACTTTCCGCTGGGGACTTTCCA

Sequence of entity 4 (J, Y), FASTA

>3GUT_4 HIV-LTR Core Reverse Strand (chains J, Y)
TTGGAAAGTCCCCAGCGGAAAGTCCC

Primary citation

Structural basis of HIV-1 activation by NF-kappaB--a higher-order complex of p50:RelA bound to the HIV-1 LTR. Stroud, J.C., Oltman, A., Han, A. et al. J Mol Biol (2009) 393:98-112. DOI 10.1016/j.jmb.2009.08.023 · PubMed

Other PDB entries of the same protein (UniProt Q04206 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6NV2 1.13 Å, 14-3-3 sigma with RelA/p65 binding site pS45 in complex with DP005
6QHL 1.2 Å, 14-3-3 sigma with RelA/p65 binding site pS45
7BI3 1.2 Å, 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-179
7BIQ 1.2 Å, 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-180
7BIW 1.2 Å, 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-187
7NV4 1.2 Å, 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-188
7NVI 1.2 Å, 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-186
7NWS 1.2 Å, 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-185
7NXS 1.2 Å, 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-184
7NXT 1.2 Å, 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-183
7NXW 1.2 Å, 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-182
7NXY 1.2 Å, 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-181

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