6CRI: PDB entry 6CRI

Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer. Determined by electron microscopy at 6.8 Å resolution. Released 1 Aug 2018.

Method: Electron microscopy
Resolution: 6.8 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1, Mus musculus
Chains: 24
Atoms: 53,049
Mol. weight: 885.69 kDa
Ligands: GTP, MG
Released: 1 Aug 2018

Explore 6CRI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6CRI contains 357 α-helices and 203 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.

Chain a: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	32
β-strand	14-19	6	32
α-helix	25-40	16
β-strand	49-52	4	32
β-strand	55-59	5	32
β-strand	66-71	6	32
α-helix	78-94	17
β-strand	99	1	33
α-helix	100-105	6
α-helix	107-117	11
β-strand	118-119	2	34
β-strand	122-123	2	34
α-helix	129-141	13

Chains b and S: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	51
β-strand	14-19	6	51
α-helix	25-40	16
β-strand	49-52	4	51
β-strand	55-59	5	51
β-strand	66-71	6	51
α-helix	78-94	17
α-helix	100-105	6
α-helix	107-117	11
β-strand	118-119	2	52
β-strand	122-123	2	52
α-helix	129-141	13

Chains B, I and J: 42 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	15-22	8
α-helix	27-42	16
α-helix	48-50	3
α-helix	51-56	6
α-helix	63-75	13
α-helix	83-85	3
α-helix	88-94	7
α-helix	100-112	13
α-helix	123-130	8
α-helix	135-151	17
α-helix	153-159	7
α-helix	161-169	9
α-helix	174-190	17
α-helix	201-211	11
α-helix	216-225	10
α-helix	234-244	11
α-helix	245-249	5
β-strand	250	1	1
α-helix	253-266	14
α-helix	275-282	8
α-helix	285-290	6
α-helix	291-293	3
α-helix	296-312	17
α-helix	322-324	3
α-helix	332-344	13
α-helix	348-350	3
α-helix	351-359	9
α-helix	367-383	17
α-helix	388-399	12
α-helix	404-420	17
α-helix	429-432	4
α-helix	442-454	13
α-helix	462-469	8
α-helix	473-475	3
α-helix	479-494	16
α-helix	500-507	8
α-helix	508-512	5
α-helix	517-532	16
α-helix	534-540	7
α-helix	547-550	4
α-helix	554-556	3
α-helix	557-564	8
β-strand	569	1	2
α-helix	570-574	5

Chains c, d and T: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	9	1	19
α-helix	10-12	3

Chain C: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	19-22	4	3
β-strand	23	1	4
α-helix	30-38	9
β-strand	51-58	8	3
β-strand	61-68	8	3
α-helix	72-74	3
α-helix	76-78	3
β-strand	90-91	2	4
α-helix	97-110	14
β-strand	123-125	3	4
α-helix	138-143	6
β-strand	155-157	3	4
β-strand	159	1	5
β-strand	164	1	5
α-helix	166-177	12

Chains G, Q and R: 41 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-15	9
α-helix	20-39	20
α-helix	46-58	13
α-helix	64-66	3
α-helix	67-74	8
α-helix	79-92	14
α-helix	95-97	3
α-helix	100-102	3
α-helix	103-110	8
α-helix	116-129	14
α-helix	132-137	6
α-helix	139-144	6
α-helix	151-167	17
α-helix	169-174	6
α-helix	188-204	17
α-helix	206-208	3
α-helix	209-212	4
α-helix	216-228	13
β-strand	236-237	2	6
β-strand	240-241	2	6
α-helix	243-255	13
α-helix	262-266	5
α-helix	268-274	7
α-helix	283-298	16
α-helix	303-318	16
α-helix	322-334	13
α-helix	340-344	5
α-helix	347-354	8
α-helix	359-372	14
α-helix	378-390	13
α-helix	394-411	18
α-helix	416-428	13
α-helix	437-447	11
α-helix	453-463	11
α-helix	470-482	13
α-helix	484-487	4
α-helix	504-514	11
α-helix	522-532	11
α-helix	544-550	7
α-helix	551-553	3
α-helix	557-571	15
α-helix	578-580	3
α-helix	582-585	4

Chains H, U and V: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	18-24	7	7
α-helix	30-37	8
β-strand	51-58	8	7
β-strand	61-68	8	7
α-helix	75-81	7
β-strand	87-93	7	7
α-helix	100-111	12
β-strand	120-126	7	7
α-helix	136-143	8
α-helix	145-147	3
β-strand	153-156	4	7
β-strand	159	1	8
α-helix	160-162	3
β-strand	164	1	8
α-helix	166-175	10

Chain K: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	19-22	4	21
β-strand	23-24	2	22
α-helix	30-38	9
β-strand	51-58	8	21
β-strand	61-68	8	21
α-helix	72-74	3
α-helix	76-78	3
β-strand	90-91	2	22
α-helix	97-110	14
β-strand	123-125	3	22
α-helix	138-143	6
β-strand	155-157	3	22
α-helix	166-177	12

6 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
Bone marrow stromal antigen 2, Protein Nef chimera	N, T, Y, Z, c, d	protein	264	Homo sapiens, Human immunodeficiency virus 1	P03404, Q10589 (AlphaFold model)
AP-1 complex subunit beta-1	B, I, J	protein	570	Homo sapiens	Q10567 (AlphaFold model)
ADP-ribosylation factor 1	C, H, K, L, U, V	protein	165	Homo sapiens	P84077 (AlphaFold model)
AP-1 complex subunit gamma-1	G, Q, R	protein	585	Mus musculus	P22892
AP-1 complex subunit mu-1	M, W, X	protein	422	Mus musculus	P35585
AP-1 complex subunit sigma-3	S, a, b	protein	142	Homo sapiens	Q96PC3

Sequence of entity 1 (N, T, Y, Z, c, d), FASTA

>6CRI_1 Bone marrow stromal antigen 2, Protein Nef chimera (chains N, T, Y, Z, c, d)
MSYYHHHHHHDYDIPTTENLYFQGAMGSASTSYDYCRVPMEDGDKRCKGSDEASEGSGMG
GKWSKSSVIGWPAVRERMRRAEPAADGVGAVSRDLEKHGAITSSNTAANNAACAWLEAQE
EEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFP
DWQNYTPGPGVRYPLTFGWCYKLVPVEPDKVEEANKGENTSLLHPVSLHGMDDPEREVLE
WRFDSRLAFHHVARELHPEYFKNC

Sequence of entity 2 (B, I, J), FASTA

>6CRI_2 AP-1 complex subunit beta-1 (chains B, I, J)
EIFELKAELNSDKKEKKKEAVKKVIASMTVGKDVSALFPDVVNCMQTDNLELKKLVYLYL
MNYAKSQPDMAIMAVNTFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDE
DPYVRKTAAVCVAKLHDINAQLVEDQGFLDTLKDLISDSNPMVVANAVAALSEIAESHPS
SNLLDLNPQSINKLLTALNECTEWGQIFILDCLANYMPKDDREAQSICERVTPRLSHANS
AVVLSAVKVLMKFMEMLSKDLDYYGTLLKKLAPPLVTLLSAEPELQYVALRNINLIVQKR
PEILKHEMKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELREYATEVDVDFVRKA
VRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIKDIFRKYPNKYESVIATLC
ENLDSLDEPEARAAMIWIVGEYAERIDNADELLESFLEGFHDKSTQVQLQLLTAIVKLFL
KKPTETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVAAKEVVLAEKPLISEETD
LIEPTLLDELICYIGTLASVYHKPPSAFVE

Sequence of entity 3 (C, H, K, L, U, V), FASTA

>6CRI_3 ADP-ribosylation factor 1 (chains C, H, K, L, U, V)
EMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGLDKIRP
LWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNA
AEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK

Sequence of entity 4 (G, Q, R), FASTA

>6CRI_4 AP-1 complex subunit gamma-1 (chains G, Q, R)
PIRLRELIRTIRTARTQAEEREMIQKECAAIRSSFREEDNTYRCRNVAKLLYMHMLGYPA
HFGQLECLKLIASQKFTDKRIGYLGAMLLLDERQDVHLLMTNCIKNDLNHSTQFVQGLAL
CTLGCMGSSEMCRDLAGEVEKLLKTSNSYLRKKAALCAVHVIRKVPELMEMFLPATKNLL
NEKNHGVLHTSVVLLTEMCERSPDMLAHFRKLVPQLVRILKNLIMSGYSPEHDVSGISDP
FLQVRILRLLRILGRNDDDSSEAMNDILAQVATNTETSKNVGNAILYETVLTIMDIKSES
GLRVLAINILGRFLLNNDKNIRYVALTSLLKTVQTDHNAVQRHRSTIVDCLKDLDVSIKR
RAMELSFALVNGNNIRGMMKELLYFLDSCEPEFKADCASGIFLAAEKYAPSKRWHIDTIM
RVLTTAGSYVRDDAVPNLIQLITNSVEMHAYTVQRLYKAILGDYSQQPLVQVAAWCIGEY
GDLLVSGQCEEEEPIQVTEDEVLDILESVLISNMSTSVTRGYALTAIMKLSTRFTCTVNR
IKKVVSIYGSSIDVELQQRAVEYNALFKKYDHMRSALLERMPVME

Sequence of entity 5 (M, W, X), FASTA

>6CRI_5 AP-1 complex subunit mu-1 (chains M, W, X)
SASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWIK
HNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDFG
YPQTTDSKILQEYITQEGHKLETGAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIEAVNL
LVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRGKSKSVELEDVKFHQC
VRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMVKAKSQF
KRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIVWSVKSFPGGKEYLMRAHFG
LPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQLR
TQ

Sequence of entity 6 (S, a, b), FASTA

>6CRI_6 AP-1 complex subunit sigma-3 (chains S, a, b)
MIHFILLFSRQGKLRLQKWYITLPDKERKKITREIVQIILSRGHRTSSFVDWKELKLVYK
RYASLYFCCAIENQDNELLTLEIVHRYVELLDKYFGNVCELDIIFNFEKAYFILDEFIIG
GEIQETSKKIAVKAIEDSDMLQ

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	6
MG	Magnesium ion	Mg	6

Primary citation

HIV-1 Nefs Are Cargo-Sensitive AP-1 Trimerization Switches in Tetherin Downregulation. Morris, K.L., Buffalo, C.Z., Sturzel, C.M. et al. Cell (2018) 174:659-671.e14. DOI 10.1016/j.cell.2018.07.004 · PubMed

Other PDB entries of the same protein (UniProt P03404), best resolution first:

3TB8 3.71 Å, Crystal structure of full-length myristoylated HIV-1 Nef
1ZEC NMR Solution structure of NEF1-25, 20 structures

Browse structure collections

About this viewer

MolViewer shows 6CRI 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.