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Theoretical Model (Jmol Viewer)

Title :   THEORETICAL MODEL OF HUMAN CCR5 WITH DISULFIDE BOND BETWEEN CYS20 AND CYS269

Authors :   S. Q. Liu, X. F. Shi, Z. R. Sun

Date :   09 Dec 02 (Deposition) - 30 Dec 02 (Release) - 30 Dec 02 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : A

Keywords :   A Bundle Of Seven Transmembrane Alpha Helices (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Q. Liu, X. F. Shi, Z. R. Sun
Characterize Dynamic Conformational Space Of Human Ccr5 Extracellular Domain By Molecular Modeling And Molecular Dynamics Simulation
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - C-C CHEMOKINE RECEPTOR TYPE 5
	Chains	:	A
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Synonym	:	CCR5, C-C CKR-5, CC-CKR-5, CCR-5


Theoretical Model	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1ND8)

(no "Site" information available for 1ND8)

Theoretical Model

No.	Residues
1	A:20	-	A:269
2	A:101	-	A:178

Theoretical Model

No.	Residues
1	Asp A:2	-	Tyr A:3
2	Ser A:17	-	Glu A:18
3	Pro A:19	-	Cys A:20
4	Ala A:92	-	Gln A:93
5	Gln A:93	-	Trp A:94
6	Thr A:99	-	Met A:100
7	Cys A:101	-	Gln A:102
8	Tyr A:127	-	Leu A:128
9	Ala A:129	-	Val A:130
10	Phe A:144	-	Gly A:145
11	Phe A:166	-	Thr A:167
12	Ser A:169	-	Gln A:170
13	Gln A:186	-	Tyr A:187
14	Arg A:223	-	Cys A:224
15	Asn A:268	-	Cys A:269
16	Ser A:270	-	Ser A:271
17	Leu A:275	-	Asp A:276
18	Gly A:301	-	Glu A:302
19	Ala A:317	-	Lys A:318
20	Ala A:331	-	Pro A:332
21	Val A:338	-	Tyr A:339
22	Val A:350	-	Gly A:351

Theoretical Model (36, 36)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_003481	Y	10	D	CCR5_HUMAN	Unclassified	---	A	Y	10	D
02	UniProt	VAR_024066	I	12	L	CCR5_HUMAN	Polymorphism	---	A	I	12	L
03	UniProt	VAR_024067	C	20	S	CCR5_HUMAN	Polymorphism	145061115	A	C	20	S
04	UniProt	VAR_011839	A	29	S	CCR5_HUMAN	Polymorphism	1800939	A	A	29	S
05	UniProt	VAR_003482	R	31	H	CCR5_HUMAN	Polymorphism	56340326	A	R	31	H
06	UniProt	VAR_003483	P	34	L	CCR5_HUMAN	Unclassified	---	A	P	34	L
07	UniProt	VAR_024068	I	42	F	CCR5_HUMAN	Polymorphism	---	A	I	42	F
08	UniProt	VAR_011840	L	55	Q	CCR5_HUMAN	Polymorphism	1799863	A	L	55	Q
09	UniProt	VAR_011841	R	60	S	CCR5_HUMAN	Polymorphism	1800940	A	R	60	S
10	UniProt	VAR_003484	K	62	R	CCR5_HUMAN	Unclassified	---	A	K	62	R
11	UniProt	VAR_003485	Y	68	H	CCR5_HUMAN	Polymorphism	758090461	A	Y	68	H
12	UniProt	VAR_024069	A	73	V	CCR5_HUMAN	Polymorphism	56198941	A	A	73	V
13	UniProt	VAR_003486	D	95	N	CCR5_HUMAN	Polymorphism	149975182	A	D	95	N
14	UniProt	VAR_003487	G	97	E	CCR5_HUMAN	Unclassified	---	A	G	97	E
15	UniProt	VAR_003488	L	122	P	CCR5_HUMAN	Unclassified	---	A	L	122	P
16	UniProt	VAR_003489	F	158	S	CCR5_HUMAN	Unclassified	---	A	F	158	S
17	UniProt	VAR_003490	Y	176	C	CCR5_HUMAN	Unclassified	---	A	Y	176	C
18	UniProt	VAR_003491	T	177	A	CCR5_HUMAN	Unclassified	---	A	T	177	A
19	UniProt	VAR_012481	C	178	R	CCR5_HUMAN	Polymorphism	199824195	A	C	178	R
20	UniProt	VAR_003492	S	185	N	CCR5_HUMAN	Unclassified	---	A	S	185	N
21	UniProt	VAR_003493	M	210	V	CCR5_HUMAN	Unclassified	---	A	M	210	V
22	UniProt	VAR_003494	Y	214	C	CCR5_HUMAN	Unclassified	---	A	Y	214	C
23	UniProt	VAR_024070	S	215	L	CCR5_HUMAN	Polymorphism	---	A	S	215	L
24	UniProt	VAR_011842	R	223	Q	CCR5_HUMAN	Polymorphism	1800452	A	R	223	Q
25	UniProt	VAR_003495	T	239	S	CCR5_HUMAN	Unclassified	---	A	T	239	S
26	UniProt	VAR_003496	L	246	P	CCR5_HUMAN	Polymorphism	143181119	A	L	246	P
27	UniProt	VAR_003497	T	288	M	CCR5_HUMAN	Polymorphism	534088482	A	T	288	M
28	UniProt	VAR_011843	G	301	V	CCR5_HUMAN	Polymorphism	1800943	A	G	301	V
29	UniProt	VAR_003498	E	302	G	CCR5_HUMAN	Unclassified	---	A	E	302	G
30	UniProt	VAR_003499	K	303	E	CCR5_HUMAN	Unclassified	---	A	K	303	E
31	UniProt	VAR_003500	N	306	S	CCR5_HUMAN	Unclassified	---	A	N	306	S
32	UniProt	VAR_003501	K	322	R	CCR5_HUMAN	Unclassified	---	A	K	322	R
33	UniProt	VAR_003502	E	333	G	CCR5_HUMAN	Unclassified	---	A	E	333	G
34	UniProt	VAR_003503	A	335	V	CCR5_HUMAN	Polymorphism	1800944	A	A	335	V
35	UniProt	VAR_003504	Y	339	F	CCR5_HUMAN	Polymorphism	1800945	A	Y	339	F
36	UniProt	VAR_003505	E	345	G	CCR5_HUMAN	Unclassified	---	A	E	345	G

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Theoretical Model (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_PROTEIN_RECEP_F1_1	PS00237	G-protein coupled receptors family 1 signature.	CCR5_HUMAN	114-130	1	A:114-130

Theoretical Model (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000292303	2b	ENSE00001078626	chr3:46412345-46412479	135	CCR5_HUMAN	-	0	0	-	-
1.3c	ENST00000292303	3c	ENSE00001054508	chr3:46414383-46417697	3315	CCR5_HUMAN	1-356	356	1	A:1-352	352

Theoretical Model

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:352
 aligned with CCR5_HUMAN | P51681 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:352
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350  
           CCR5_HUMAN     1 MDYQVSSPIYDINYYTSEPCQKINVKQIAARLLPPLYSLVFIFGFVGNMLVILILINCKRLKSMTDIYLLNLAISDLFFLLTVPFWAHYAAAQWDFGNTMCQLLTGLYFIGFFSGIFFIILLTIDRYLAVVHAVFALKARTVTFGVVTSVITWVVAVFASLPGIIFTRSQKEGLHYTCSSHFPYSQYQFWKNFQTLKIVILGLVLPLLVMVICYSGILKTLLRCRNEKKRHRAVRLIFTIMIVYFLFWAPYNIVLLLNTFQEFFGLNNCSSSNRLDQAMQVTETLGMTHCCINPIIYAFVGEKFRNYLLVFFQKHIAKRFCKCCSIFQQEAPERASSVYTRSTGEQEISVGL 352
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............................hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhh.........................hhhhhhhhh..hhhhh.................................hhhhhhh.hhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhh...................................................... Sec.struct. author
                 SAPs(SNPs) ---------D-L-------S--------S-H--L-------F------------Q----S-R-----H----V---------------------N-E------------------------P-----------------------------------S-----------------CAR------N------------------------V---CL-------Q---------------S------P-----------------------------------------M------------VGE--S---------------R----------G-V---F-----G------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------G_PROTEIN_RECEP_F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.3c  PDB: A:1-352 UniProt: 1-356 [INCOMPLETE]                                                                                                                                                                                                                                                                                                              Transcript 1
                 1nd8 A   1 MDYQVSSPIYDINYYTSEPCQKINVKQIAARLLPPLYSLVFIFGFVGNMLVILILINCKRLKSMTDIYLLNLAISDLFFLLTVPFWAHYAAAQWDFGNTMCQLLTGLYFIGFFSGIFFIILLTIDRYLAVVHAVFALKARTVTFGVVTSVITWVVAVFASLPGIIFTRSQKEGLHYTCSSHFPYSQYQFWKNFQTLKIVILGLVLPLLVMVICYSGILKTLLRCRNEKKRHRAVRLIFTIMIVYFLFWAPYNIVLLLNTFQEFFGLNNCSSSNRLDQAMQVTETLGMTHCCINPIIYAFVGEKFRNYLLVFFQKHIAKRFCKCCSIFQQEAPERASSVYTRSTGEQEISVGL 352
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 1ND8)

(no "CATH Domain" information available for 1ND8)

(no "Pfam Domain" information available for 1ND8)

Theoretical Model(hide GO term definitions)

Chain A (CCR5_HUMAN | P51681)

molecular function
	GO:0019957	C-C chemokine binding	Interacting selectively and non-covalently with a C-C chemokine; C-C chemokines do not have an amino acid between the first two cysteines of the characteristic four-cysteine motif.
	GO:0016493	C-C chemokine receptor activity	Combining with a C-C chemokine and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. C-C chemokines do not have an amino acid between the first two cysteines of the characteristic four-cysteine motif.
	GO:0004930	G-protein coupled receptor activity	Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0071791	chemokine (C-C motif) ligand 5 binding	Interacting selectively and non-covalently with chemokine (C-C motif) ligand 5.
	GO:0004950	chemokine receptor activity	Combining with a chemokine, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. Chemokines are a family of small chemotactic cytokines; their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria.
	GO:0015026	coreceptor activity	Combining with an extracellular or intracellular messenger, and in cooperation with a nearby primary receptor, initiating a change in cell activity.
	GO:0004435	phosphatidylinositol phospholipase C activity	Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H(2)O = 1,2-diacylglycerol + 1D-myo-inositol 1,4,5-trisphosphate + H(+).
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
	GO:0001618	virus receptor activity	Combining with a virus component and mediating entry of the virus into the cell.
biological process
	GO:0007186	G-protein coupled receptor signaling pathway	A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
	GO:0000165	MAPK cascade	An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
	GO:0006816	calcium ion transport	The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0019722	calcium-mediated signaling	Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions.
	GO:0007166	cell surface receptor signaling pathway	A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0007267	cell-cell signaling	Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
	GO:0006968	cellular defense response	A defense response that is mediated by cells.
	GO:0071222	cellular response to lipopolysaccharide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0070098	chemokine-mediated signaling pathway	A series of molecular signals initiated by the binding of a chemokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0006935	chemotaxis	The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	GO:0002407	dendritic cell chemotaxis	The movement of a dendritic cell in response to an external stimulus.
	GO:0030260	entry into host cell	The invasion by an organism of a cell of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0019064	fusion of virus membrane with host plasma membrane	Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
	GO:0007204	positive regulation of cytosolic calcium ion concentration	Any process that increases the concentration of calcium ions in the cytosol.
	GO:0014808	release of sequestered calcium ion into cytosol by sarcoplasmic reticulum	The process in which the release of sequestered calcium ion by sarcoplasmic reticulum into cytosol occurs via calcium release channels.
	GO:0070723	response to cholesterol	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cholesterol stimulus.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0023052	signaling	The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Theoretical Model
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1nd8)

	Sites
(no "Sites" information available for 1nd8)

	Cis Peptide Bonds
		Ala A:129 - Val A:130	[ RasMol ]
		Ala A:317 - Lys A:318	[ RasMol ]
		Ala A:331 - Pro A:332	[ RasMol ]
		Ala A:92 - Gln A:93	[ RasMol ]
		Arg A:223 - Cys A:224	[ RasMol ]
		Asn A:268 - Cys A:269	[ RasMol ]
		Asp A:2 - Tyr A:3	[ RasMol ]
		Cys A:101 - Gln A:102	[ RasMol ]
		Gln A:186 - Tyr A:187	[ RasMol ]
		Gln A:93 - Trp A:94	[ RasMol ]
		Gly A:301 - Glu A:302	[ RasMol ]
		Leu A:275 - Asp A:276	[ RasMol ]
		Phe A:144 - Gly A:145	[ RasMol ]
		Phe A:166 - Thr A:167	[ RasMol ]
		Pro A:19 - Cys A:20	[ RasMol ]
		Ser A:169 - Gln A:170	[ RasMol ]
		Ser A:17 - Glu A:18	[ RasMol ]
		Ser A:270 - Ser A:271	[ RasMol ]
		Thr A:99 - Met A:100	[ RasMol ]
		Tyr A:127 - Leu A:128	[ RasMol ]
		Val A:338 - Tyr A:339	[ RasMol ]
		Val A:350 - Gly A:351	[ RasMol ]

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	1nd8
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	CCR5_HUMAN \| P51681
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UniProtKB/Swiss-Prot
	CCR5_HUMAN \| P51681	:	1ne0 1opn 1opt 1opw 2l87 2mzx 2rll 2rrs 4mbs 5uiw

1f88	CRYSTAL STRUCTURE OF RHODOPSIN:A G PROTEINCCOUPLED RECEPTOR, WHICH IS SELECTED AS THE TEMPLATE IN BUILDING THE TRANSMEMBRANE REGIONS OF CCR5 MODEL.
1ne0	THEORETICAL MODEL OF HUMAN CCR5 WITH DISULFIDE BOND BETWEEN CYS20 AND CYS269

Description

Compounds

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (22, 22)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (36, 36)

PROSITE Motifs (1, 1)

Exons (1, 1)

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Gene Ontology (40, 40)

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