1K8F - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE HUMAN C-TERMINAL CAP1-ADENYLYL CYCLASE ASSOCIATED PROTEIN

Authors :   Y. V. Patskovsky, M. Chance, S. C. Almo, S. K. Burley, New York Sgx Res Center For Structural Genomics (Nysgxrc)

Date :   24 Oct 01 (Deposition) - 01 Jul 03 (Release) - 25 Jan 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Cap, Cap1, Adenylyl Cyclase Associated Protein, Actin Binding, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Dodatko, A. A. Fedorov, M. Grynberg, Y. Patskovsky, D. A. Rozwarski L. Jaroszewski, E. Aronoff-Spencer, E. Kondraskina, T. Irving, A. Godzik, S. C. Almo
Crystal Structure Of The Actin Binding Domain Of The Cyclase-Associated Protein.
Biochemistry V. 43 10628 2004
PubMed-ID: 15311924 | Reference-DOI: 10.1021/BI049071R

Molecule 1 - ADENYLYL CYCLASE-ASSOCIATED PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PCRTOPO-NT
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN
	Gene	:	CAP1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CAP

		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 1K8F)

(no "Site" information available for 1K8F)

(no "SS Bond" information available for 1K8F)

(no "Cis Peptide Bond" information available for 1K8F)

(no "SAP(SNP)/Variant" information available for 1K8F)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_CAP_COFACTOR_C	PS51329	C-CAP/cofactor C-like domain profile.	CAP1_HUMAN	319-453	4	A:319-453 B:319-453 C:319-453 D:319-453
2	CAP_2	PS01089	CAP protein signature 2.	CAP1_HUMAN	447-458	4	A:447-458 B:447-458 C:447-458 D:447-458

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_CAP_COFACTOR_C	PS51329	C-CAP/cofactor C-like domain profile.	CAP1_HUMAN	319-453	2	A:319-453 B:319-453 - -
2	CAP_2	PS01089	CAP protein signature 2.	CAP1_HUMAN	447-458	2	A:447-458 B:447-458 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_CAP_COFACTOR_C	PS51329	C-CAP/cofactor C-like domain profile.	CAP1_HUMAN	319-453	2	- - C:319-453 D:319-453
2	CAP_2	PS01089	CAP protein signature 2.	CAP1_HUMAN	447-458	2	- - C:447-458 D:447-458

Asymmetric Unit (5, 20)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1k	ENST00000372805	1k	ENSE00001822157	chr1:40506433-40506473	41	CAP1_HUMAN	-	0	0	-	-
1.5b	ENST00000372805	5b	ENSE00001458701	chr1:40525009-40525130	122	CAP1_HUMAN	1-38	38	0	-	-
1.6c	ENST00000372805	6c	ENSE00000899727	chr1:40525739-40525842	104	CAP1_HUMAN	38-72	35	0	-	-
1.7	ENST00000372805	7	ENSE00001192144	chr1:40527407-40527484	78	CAP1_HUMAN	73-98	26	0	-	-
1.9a	ENST00000372805	9a	ENSE00001192143	chr1:40529899-40530042	144	CAP1_HUMAN	99-146	48	0	-	-
1.10b	ENST00000372805	10b	ENSE00001192141	chr1:40530146-40530231	86	CAP1_HUMAN	147-175	29	0	-	-
1.11f	ENST00000372805	11f	ENSE00001192138	chr1:40531887-40531992	106	CAP1_HUMAN	175-210	36	0	-	-
1.13c	ENST00000372805	13c	ENSE00001080383	chr1:40533212-40533389	178	CAP1_HUMAN	211-270	60	0	-	-
1.14c	ENST00000372805	14c	ENSE00002162881	chr1:40535362-40535546	185	CAP1_HUMAN	270-331	62	4	A:319-331 B:319-331 C:319-331 D:319-331	13 13 13 13
1.15	ENST00000372805	15	ENSE00001617664	chr1:40535831-40535954	124	CAP1_HUMAN	332-373	42	4	A:332-373 B:332-373 C:332-373 D:332-373	42 42 42 42
1.16a	ENST00000372805	16a	ENSE00001616471	chr1:40536102-40536184	83	CAP1_HUMAN	373-400	28	4	A:373-400 B:373-400 C:373-400 D:373-400	28 28 28 28
1.16c	ENST00000372805	16c	ENSE00001698223	chr1:40536508-40536651	144	CAP1_HUMAN	401-448	48	4	A:401-448 B:401-448 C:401-448 D:401-448	48 48 48 48
1.17g	ENST00000372805	17g	ENSE00001937537	chr1:40537122-40537943	822	CAP1_HUMAN	449-475	27	4	A:449-475 B:449-475 C:449-475 D:449-475	27 27 27 27

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:157
 aligned with CAP1_HUMAN | Q01518 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:157
                                   328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       
           CAP1_HUMAN   319 PAVLELEGKKWRVENQENVSNLVIEDTELKQVAYIYKCVNTTLQIKGKINSITVDNCKKLGLVFDDVVGIVEIINSKDVKVQVMGKVPTISINKTDGCHAYLSKNSLDCEIVSAKSSEMNVLIPTEGGDFNEFPVPEQFKTLWNGQKLVTTVTEIAG 475
               SCOP domains d1k8fa_ A: C-terminal domain of adenylylcyclase associated protein                                                                                            SCOP domains
               CATH domains 1k8fA00 A:319-475  [code=2.160.20.70, no name defined]                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeeee.......eee.......eeeee.....eeeeeeee.eeeee..eeeeeeeeee..eeeee..eeeeeee.....eeeee..eeeeee........eeeee..eeeeeeeee...eeeeee...eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) C_CAP_COFACTOR_C  PDB: A:319-453 UniProt: 319-453                                                                                      ---------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------CAP_2       ----------------- PROSITE (2)
           Transcript 1 (1) Exon 1.14c   Exon 1.15  PDB: A:332-373 UniProt: 332-373---------------------------Exon 1.16c  PDB: A:401-448 UniProt: 401-448     Exon 1.17g  PDB: A:449-475  Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.16a  PDB: A:373-400  --------------------------------------------------------------------------- Transcript 1 (2)
                 1k8f A 319 PAVLELEGKKWRVENQENVSNLVIEDTELKQVAYIYKCVNTTLQIKGKINSITVDNCKKLGLVFDDVVGIVEIINSKDVKVQVMGKVPTISINKTDGCHAYLSKNSLDCEIVSAKSSEMNVLIPTEGGDFNEFPVPEQFKTLWNGQKLVTTVTEIAG 475
                                   328       338       348       358       368       378       388       398       408       418       428       438       448       458       468

Chain B from PDB  Type:PROTEIN  Length:157
 aligned with CAP1_HUMAN | Q01518 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:157
                                   328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       
           CAP1_HUMAN   319 PAVLELEGKKWRVENQENVSNLVIEDTELKQVAYIYKCVNTTLQIKGKINSITVDNCKKLGLVFDDVVGIVEIINSKDVKVQVMGKVPTISINKTDGCHAYLSKNSLDCEIVSAKSSEMNVLIPTEGGDFNEFPVPEQFKTLWNGQKLVTTVTEIAG 475
               SCOP domains d1k8fb_ B: C-terminal domain of adenylylcyclase associated protein                                                                                            SCOP domains
               CATH domains 1k8fB00 B:319-475  [code=2.160.20.70, no name defined]                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeeee.......eee.......eeeee..eeeeeeeeeee.eeeee..eeeeeeeeee..eeeee..eeeeeee.....eeeee..eeeeee........eeeee..eeeeeeeee...eeeeee...eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) C_CAP_COFACTOR_C  PDB: B:319-453 UniProt: 319-453                                                                                      ---------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------CAP_2       ----------------- PROSITE (2)
           Transcript 1 (1) Exon 1.14c   Exon 1.15  PDB: B:332-373 UniProt: 332-373---------------------------Exon 1.16c  PDB: B:401-448 UniProt: 401-448     Exon 1.17g  PDB: B:449-475  Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.16a  PDB: B:373-400  --------------------------------------------------------------------------- Transcript 1 (2)
                 1k8f B 319 PAVLELEGKKWRVENQENVSNLVIEDTELKQVAYIYKCVNTTLQIKGKINSITVDNCKKLGLVFDDVVGIVEIINSKDVKVQVMGKVPTISINKTDGCHAYLSKNSLDCEIVSAKSSEMNVLIPTEGGDFNEFPVPEQFKTLWNGQKLVTTVTEIAG 475
                                   328       338       348       358       368       378       388       398       408       418       428       438       448       458       468

Chain C from PDB  Type:PROTEIN  Length:157
 aligned with CAP1_HUMAN | Q01518 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:157
                                   328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       
           CAP1_HUMAN   319 PAVLELEGKKWRVENQENVSNLVIEDTELKQVAYIYKCVNTTLQIKGKINSITVDNCKKLGLVFDDVVGIVEIINSKDVKVQVMGKVPTISINKTDGCHAYLSKNSLDCEIVSAKSSEMNVLIPTEGGDFNEFPVPEQFKTLWNGQKLVTTVTEIAG 475
               SCOP domains d1k8fc_ C: C-terminal domain of adenylylcyclase associated protein                                                                                            SCOP domains
               CATH domains 1k8fC00 C:319-475  [code=2.160.20.70, no name defined]                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeeee.......eee.......eeeee.....eeeeeeee.eeeee..eeeeeeeeee..eeeee..eeeeeee.....eeeee..eeeeee........eeeee..eeeeeeeee...eeeeeee..eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) C_CAP_COFACTOR_C  PDB: C:319-453 UniProt: 319-453                                                                                      ---------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------CAP_2       ----------------- PROSITE (2)
           Transcript 1 (1) Exon 1.14c   Exon 1.15  PDB: C:332-373 UniProt: 332-373---------------------------Exon 1.16c  PDB: C:401-448 UniProt: 401-448     Exon 1.17g  PDB: C:449-475  Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.16a  PDB: C:373-400  --------------------------------------------------------------------------- Transcript 1 (2)
                 1k8f C 319 PAVLELEGKKWRVENQENVSNLVIEDTELKQVAYIYKCVNTTLQIKGKINSITVDNCKKLGLVFDDVVGIVEIINSKDVKVQVMGKVPTISINKTDGCHAYLSKNSLDCEIVSAKSSEMNVLIPTEGGDFNEFPVPEQFKTLWNGQKLVTTVTEIAG 475
                                   328       338       348       358       368       378       388       398       408       418       428       438       448       458       468

Chain D from PDB  Type:PROTEIN  Length:157
 aligned with CAP1_HUMAN | Q01518 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:157
                                   328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       
           CAP1_HUMAN   319 PAVLELEGKKWRVENQENVSNLVIEDTELKQVAYIYKCVNTTLQIKGKINSITVDNCKKLGLVFDDVVGIVEIINSKDVKVQVMGKVPTISINKTDGCHAYLSKNSLDCEIVSAKSSEMNVLIPTEGGDFNEFPVPEQFKTLWNGQKLVTTVTEIAG 475
               SCOP domains d1k8fd_ D: C-terminal domain of adenylylcyclase associated protein                                                                                            SCOP domains
               CATH domains 1k8fD00 D:319-475  [code=2.160.20.70, no name defined]                                                                                                        CATH domains
           Pfam domains (1) CAP_C-1k8fD01 D:319-474                                                                                                                                     - Pfam domains (1)
           Pfam domains (2) CAP_C-1k8fD02 D:319-474                                                                                                                                     - Pfam domains (2)
           Pfam domains (3) CAP_C-1k8fD03 D:319-474                                                                                                                                     - Pfam domains (3)
           Pfam domains (4) CAP_C-1k8fD04 D:319-474                                                                                                                                     - Pfam domains (4)
         Sec.struct. author ..eeeee..eeeee.......eee.......eeeee.....eeeeeeee.eeeee..eeeeeeeeee..eeeee..eeeeeee.....eeeee..eeeeee........eeeee..eeeeeeeee...eeeeee...eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) C_CAP_COFACTOR_C  PDB: D:319-453 UniProt: 319-453                                                                                      ---------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------CAP_2       ----------------- PROSITE (2)
           Transcript 1 (1) Exon 1.14c   Exon 1.15  PDB: D:332-373 UniProt: 332-373---------------------------Exon 1.16c  PDB: D:401-448 UniProt: 401-448     Exon 1.17g  PDB: D:449-475  Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.16a  PDB: D:373-400  --------------------------------------------------------------------------- Transcript 1 (2)
                 1k8f D 319 PAVLELEGKKWRVENQENVSNLVIEDTELKQVAYIYKCVNTTLQIKGKINSITVDNCKKLGLVFDDVVGIVEIINSKDVKVQVMGKVPTISINKTDGCHAYLSKNSLDCEIVSAKSSEMNVLIPTEGGDFNEFPVPEQFKTLWNGQKLVTTVTEIAG 475
                                   328       338       348       358       368       378       388       398       408       418       428       438       448       458       468

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: 3 Solenoid (196)

Topology: Pectate Lyase C-like (105)

Homologous Superfamily: [code=2.160.20.70, no name defined] (5)

Human (Homo sapiens) (1)

1a	1k8fA00	A:319-475
1b	1k8fB00	B:319-475
1c	1k8fC00	C:319-475
1d	1k8fD00	D:319-475

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CAP_C-like (4)

Family: CAP_C (3)

Homo sapiens (Human) (1)

1a	CAP_C-1k8fD01	D:319-474
1b	CAP_C-1k8fD02	D:319-474
1c	CAP_C-1k8fD03	D:319-474
1d	CAP_C-1k8fD04	D:319-474

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CAP1_HUMAN | Q01518)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
biological process
	GO:0030036	actin cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
	GO:0007190	activation of adenylate cyclase activity	Any process that initiates the activity of the inactive enzyme adenylate cyclase.
	GO:0001667	ameboidal-type cell migration	Cell migration that is accomplished by extension and retraction of a pseudopodium.
	GO:0000902	cell morphogenesis	The developmental process in which the size or shape of a cell is generated and organized.
	GO:0007010	cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
	GO:0007163	establishment or maintenance of cell polarity	Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns.
	GO:0006898	receptor-mediated endocytosis	An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
	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.
cellular component
	GO:0030864	cortical actin cytoskeleton	The portion of the actin cytoskeleton, comprising filamentous actin and associated proteins, that lies just beneath the plasma membrane.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	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.

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1k4z	YEAST ADENYLYL CYCLASE ASSOCIATED PROTEIN (CAP), C-TERMINAL DOMAIN RELATED ID: NYSGXRC-T139 RELATED DB: TARGETDB

Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

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PROSITE Motifs (2, 8)

Exons (5, 20)

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SCOP Domains (1, 4)

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