2FJ2 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF VIRAL MACROPHAGE INFLAMMATORY PROTEIN-II

Authors :   Y. Li, D. Liu, R. Cao, S. Kumar, C. Z. Dong, S. R. Wilson, Y. G. Gao, Z. Huang

Date :   30 Dec 05 (Deposition) - 26 Dec 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Chemokine, Herpesvirus, Anti-Hiv (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Li, D. Liu, R. Cao, S. Kumar, C. Dong, J. An, S. R. Wilson, Y. G. Gao, Z. Huang
Crystal Structure Of Chemically Synthesized Vmip-Ii.
Proteins V. 67 243 2007
PubMed-ID: 17243149 | Reference-DOI: 10.1002/PROT.21172
(for further references see the PDB file header)

Molecule 1 - VIRAL MACROPHAGE INFLAMMATORY PROTEIN-II
	Chains	:	A, B, C, D
	Engineered	:	YES
	Other Details	:	SEQUENCE OCCURS IN KAPOSI'S SARCOMA HERPES VIRUS-8
	Synonym	:	VMIP-II, VMIP- 1B
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2FJ2)

(no "Site" information available for 2FJ2)

Asymmetric Unit

No.	Residues
1	A:11	-	A:35
2	A:12	-	A:51
3	B:11	-	B:35
4	B:12	-	B:51
5	C:11	-	C:35
6	C:12	-	C:51
7	D:11	-	D:35
8	D:12	-	D:51

(no "Cis Peptide Bond" information available for 2FJ2)

(no "SAP(SNP)/Variant" information available for 2FJ2)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SMALL_CYTOKINES_CC	PS00472	Small cytokines (intercrine/chemokine) C-C subfamily signature.	VMI2_HHV8P	34-75	4	A:11-52 B:11-52 C:11-52 D:11-52

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SMALL_CYTOKINES_CC	PS00472	Small cytokines (intercrine/chemokine) C-C subfamily signature.	VMI2_HHV8P	34-75	2	A:11-52 B:11-52 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SMALL_CYTOKINES_CC	PS00472	Small cytokines (intercrine/chemokine) C-C subfamily signature.	VMI2_HHV8P	34-75	2	- - C:11-52 D:11-52

(no "Exon" information available for 2FJ2)

Asymmetric Unit

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:68
 aligned with VMI2_HHV8P | Q98157 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:68
                                    36        46        56        66        76        86        
            VMI2_HHV8P   27 SWHRPDKCCLGYQKRPLPQVLLSSWYPTSQLCSKPGVIFLTKRGRQVCADKSKDWVKKLMQQLPVTAR 94
               SCOP domains d2fj2a1 A:4-71 Macrophage inflammatory protein, MIP                  SCOP domains
               CATH domains 2fj2A00 A:4-71  [code=2.40.50.40, no name defined]                   CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.........hhh.eeeeee.........eeeee....eeee...hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------SMALL_CYTOKINES_CC  PDB: A:11-52          ------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2fj2 A  4 SWHRPDKCCLGYQKRPLPQVLLSSWYPTSQLCSKPGVIFLTKRGRQVCADKSKDWVKKLMQQLPVTAR 71
                                    13        23        33        43        53        63

Chain B from PDB  Type:PROTEIN  Length:67
 aligned with VMI2_HHV8P | Q98157 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:67
                                    37        47        57        67        77        87       
            VMI2_HHV8P   28 WHRPDKCCLGYQKRPLPQVLLSSWYPTSQLCSKPGVIFLTKRGRQVCADKSKDWVKKLMQQLPVTAR 94
               SCOP domains d2fj2b1 B:5-71 Macrophage inflammatory protein, MIP                 SCOP domains
               CATH domains 2fj2B00 B:5-71  [code=2.40.50.40, no name defined]                  CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.........hhh.eeeeee........eeeeee....eeeee..hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------SMALL_CYTOKINES_CC  PDB: B:11-52          ------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  2fj2 B  5 WHRPDKCCLGYQKRPLPQVLLSSWYPTSQLCSKPGVIFLTKRGRQVCADKSKDWVKKLMQQLPVTAR 71
                                    14        24        34        44        54        64

Chain C from PDB  Type:PROTEIN  Length:68
 aligned with VMI2_HHV8P | Q98157 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:68
                                    36        46        56        66        76        86        
            VMI2_HHV8P   27 SWHRPDKCCLGYQKRPLPQVLLSSWYPTSQLCSKPGVIFLTKRGRQVCADKSKDWVKKLMQQLPVTAR 94
               SCOP domains d2fj2c1 C:4-71 Macrophage inflammatory protein, MIP                  SCOP domains
               CATH domains 2fj2C00 C:4-71  [code=2.40.50.40, no name defined]                   CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.........hhh.eeeeee.........eeeee....eeee...hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------SMALL_CYTOKINES_CC  PDB: C:11-52          ------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2fj2 C  4 SWHRPDKCCLGYQKRPLPQVLLSSWYPTSQLCSKPGVIFLTKRGRQVCADKSKDWVKKLMQQLPVTAR 71
                                    13        23        33        43        53        63

Chain D from PDB  Type:PROTEIN  Length:67
 aligned with VMI2_HHV8P | Q98157 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:67
                                    37        47        57        67        77        87       
            VMI2_HHV8P   28 WHRPDKCCLGYQKRPLPQVLLSSWYPTSQLCSKPGVIFLTKRGRQVCADKSKDWVKKLMQQLPVTAR 94
               SCOP domains d2fj2d1 D:5-71 Macrophage inflammatory protein, MIP                 SCOP domains
               CATH domains 2fj2D00 D:5-71  [code=2.40.50.40, no name defined]                  CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.........hhh.eeeeee.........eeeee....eeee...hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------SMALL_CYTOKINES_CC  PDB: D:11-52          ------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  2fj2 D  5 WHRPDKCCLGYQKRPLPQVLLSSWYPTSQLCSKPGVIFLTKRGRQVCADKSKDWVKKLMQQLPVTAR 71
                                    14        24        34        44        54        64

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: IL8-like (118)

Superfamily: Interleukin 8-like chemokines (117)

Family: Interleukin 8-like chemokines (113)

Protein domain: Macrophage inflammatory protein, MIP (17)

Kaposi's sarcoma-associated herpesvirus, VMIP-II [TaxId: 37296] (7)

1a	d2fj2a1	A:4-71
1b	d2fj2b1	B:5-71
1c	d2fj2c1	C:4-71
1d	d2fj2d1	D:5-71

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: [code=2.40.50.40, no name defined] (161)

[unclassified] (41)

1a	2fj2B00	B:5-71
1b	2fj2D00	D:5-71
1c	2fj2A00	A:4-71
1d	2fj2C00	C:4-71

(no "Pfam Domain" information available for 2FJ2)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (VMI2_HHV8P | Q98157)

molecular function
	GO:0008009	chemokine activity	The function of 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:0005125	cytokine activity	Functions to control the survival, growth, differentiation and effector function of tissues and cells.
biological process
	GO:0060326	cell chemotaxis	The directed movement of a motile 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:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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	VMI2_HHV8P \| Q98157	:	1cm9 1hff 1hfg 1hfn 1hhv 1vmp 2fht 4rws

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SS Bonds (8, 8)

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