3JUE - JenaLib

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Title :   CRYSTAL STRUCTURE OF ARFGAP AND ANK REPEAT DOMAIN OF ACAP1

Authors :   X. Pang, K. Zhang, J. Ma, Q. Zhou, F. Sun

Date :   15 Sep 09 (Deposition) - 22 Sep 10 (Release) - 16 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Arfgap Domain, Ank Repeat, Zinc-Binding Module, Gtpase Activation, Metal-Binding, Nitration, Phosphoprotein, Protein Transport, Transport, Zinc-Finger, Protein Transport-Endocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Bai, X. Pang, J. Lou, Q. Zhou, K. Zhang, J. Ma, J. Li, F. Sun, V. W. Hsu
Mechanistic Insights Into Regulated Cargo Binding By Acap1 Protein
J. Biol. Chem. V. 287 28675 2012
PubMed-ID: 22645133 | Reference-DOI: 10.1074/JBC.M112.378810

Molecule 1 - ARFGAP WITH COILED-COIL, ANK REPEAT AND PH DOMAIN- CONTAINING PROTEIN 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	ARFGAP AND ANK REPEAT DOMAIN, RESIDUES 378-740
	Gene	:	ACAP1, CENTB1, KIAA0050
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CENTAURIN-BETA-1, CNT-B1

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:420 , CYS A:423 , CYS A:440 , CYS A:443	BINDING SITE FOR RESIDUE ZN A 999
2	AC2	SOFTWARE	HIS A:570 , PRO A:571 , GLY A:572 , ALA A:573 , TRP A:600	BINDING SITE FOR RESIDUE SO4 A 1133
3	AC3	SOFTWARE	TRP A:430 , ILE A:441 , SER A:444 , GLY A:445 , ARG A:448 , GLN B:412 , SER B:413	BINDING SITE FOR RESIDUE SO4 A 1135
4	AC4	SOFTWARE	CYS B:420 , CYS B:423 , CYS B:440 , CYS B:443	BINDING SITE FOR RESIDUE ZN B 999
5	AC5	SOFTWARE	HIS B:570 , PRO B:571 , GLY B:572 , ALA B:573 , TRP B:600 , HOH B:1042	BINDING SITE FOR RESIDUE SO4 B 1134

(no "SS Bond" information available for 3JUE)

Asymmetric Unit

No.	Residues
1	His A:581	-	Pro A:582
2	His B:581	-	Pro B:582

(no "SAP(SNP)/Variant" information available for 3JUE)

Asymmetric Unit (3, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARFGAP	PS50115	ARF GTPase-activating proteins domain profile.	ACAP1_HUMAN	405-527	2	A:405-524 B:405-524
2	ANK_REP_REGION	PS50297	Ankyrin repeat region circular profile.	ACAP1_HUMAN	592-692	2	A:592-692 B:592-692
3	ANK_REPEAT	PS50088	Ankyrin repeat profile.	ACAP1_HUMAN	606-638 639-671	4	A:606-638 B:606-638 A:639-671 B:639-671

Biological Unit 1 (3, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARFGAP	PS50115	ARF GTPase-activating proteins domain profile.	ACAP1_HUMAN	405-527	1	A:405-524 -
2	ANK_REP_REGION	PS50297	Ankyrin repeat region circular profile.	ACAP1_HUMAN	592-692	1	A:592-692 -
3	ANK_REPEAT	PS50088	Ankyrin repeat profile.	ACAP1_HUMAN	606-638 639-671	2	A:606-638 - A:639-671 -

Biological Unit 2 (3, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARFGAP	PS50115	ARF GTPase-activating proteins domain profile.	ACAP1_HUMAN	405-527	1	- B:405-524
2	ANK_REP_REGION	PS50297	Ankyrin repeat region circular profile.	ACAP1_HUMAN	592-692	1	- B:592-692
3	ANK_REPEAT	PS50088	Ankyrin repeat profile.	ACAP1_HUMAN	606-638 639-671	2	- B:606-638 - B:639-671

(no "Exon" information available for 3JUE)

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:250
 aligned with ACAP1_HUMAN | Q15027 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:294
                                   413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693    
          ACAP1_HUMAN   404 VGHVVAQVQSVDGNAQCCDCREPAPEWASINLGVTLCIQCSGIHRSLGVHFSKVRSLTLDSWEPELVKLMCELGNVIINQIYEARVEAMAVKKPGPSCSRQEKEAWIHAKYVEKKFLTKLPEIRGRRGGRGRPRGQPPVPPKPSIRPRPGSLRSKPEPPSEDLGSLHPGALLFRASGHPPSLPTMADALAHGADVNWVNGGQDNATPLIQATAANSLLACEFLLQNGANVNQADSAGRGPLHHATILGHTGLACLFLKRGADLGARDSEGRDPLTIAMETANADIVTLLRLAKM 697
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhh................eee....eeehhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhh.........--------------------------------------------.hhhhhhhhhh....hhhhhhhhhhh..............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -ARFGAP  PDB: A:405-524 UniProt: 405-527                                                                                    ----------------------------------------------------------------ANK_REP_REGION  PDB: A:592-692 UniProt: 592-692                                                      ----- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ANK_REPEAT  PDB: A:606-638       ANK_REPEAT  PDB: A:639-671       -------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3jue A 404 VGHVVAQVQSVDGNAQCCDCREPAPEWASINLGVTLCIQCSGIHRSLGVHFSKVRSLTLDSWEPELVKLMCELGNVIINQIYEARVEAMAVKKPGPSCSRQEKEAWIHAKYVEKKFLTKLP--------------------------------------------LHPGALLFRASGHPPSLPTMADALAHGADVNWVNGGQDNATPLIQATAANSLLACEFLLQNGANVNQADSAGRGPLHHATILGHTGLACLFLKRGADLGARDSEGRDPLTIAMETANADIVTLLRLAKM 697
                                   413       423       433       443       453       463       473       483       493       503       513       523|        -         -         -         -     | 573       583       593       603       613       623       633       643       653       663       673       683       693    
                                                                                                                                                  524                                          569

Chain B from PDB  Type:PROTEIN  Length:254
 aligned with ACAP1_HUMAN | Q15027 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:298
                                   413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693        
          ACAP1_HUMAN   404 VGHVVAQVQSVDGNAQCCDCREPAPEWASINLGVTLCIQCSGIHRSLGVHFSKVRSLTLDSWEPELVKLMCELGNVIINQIYEARVEAMAVKKPGPSCSRQEKEAWIHAKYVEKKFLTKLPEIRGRRGGRGRPRGQPPVPPKPSIRPRPGSLRSKPEPPSEDLGSLHPGALLFRASGHPPSLPTMADALAHGADVNWVNGGQDNATPLIQATAANSLLACEFLLQNGANVNQADSAGRGPLHHATILGHTGLACLFLKRGADLGARDSEGRDPLTIAMETANADIVTLLRLAKMREAE 701
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -ArfGap-3jueB05 B:405-523                                                                                               -------------------------------------------------------------------------------------------------------------------Ank-3jueB01 B:639-671            ------------------------------ Pfam domains (1)
           Pfam domains (2) -ArfGap-3jueB06 B:405-523                                                                                               -------------------------------------------------------------------------------------------------------------------Ank-3jueB02 B:639-671            ------------------------------ Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ank-3jueB03 B:639-671            ------------------------------ Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ank-3jueB04 B:639-671            ------------------------------ Pfam domains (4)
         Sec.struct. author .hhhhhhhhh................eee....eeehhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhhhhhh.hhhhhh........hhhhhhhhhhhhhh.........--------------------------------------------.hhhhhhhhhhh...hhhhhhhhhhh..............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ARFGAP  PDB: B:405-524 UniProt: 405-527                                                                                    ----------------------------------------------------------------ANK_REP_REGION  PDB: B:592-692 UniProt: 592-692                                                      --------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ANK_REPEAT  PDB: B:606-638       ANK_REPEAT  PDB: B:639-671       ------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jue B 404 VGHVVAQVQSVDGNAQCCDCREPAPEWASINLGVTLCIQCSGIHRSLGVHFSKVRSLTLDSWEPELVKLMCELGNVIINQIYEARVEAMAVKKPGPSCSRQEKEAWIHAKYVEKKFLTKLP--------------------------------------------LHPGALLFRASGHPPSLPTMADALAHGADVNWVNGGQDNATPLIQATAANSLLACEFLLQNGANVNQADSAGRGPLHHATILGHTGLACLFLKRGADLGARDSEGRDPLTIAMETANADIVTLLRLAKMREAE 701
                                   413       423       433       443       453       463       473       483       493       503       513       523|        -         -         -         -     | 573       583       593       603       613       623       633       643       653       663       673       683       693        
                                                                                                                                                  524                                          569

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 3JUE)

(no "CATH Domain" information available for 3JUE)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ank (35)

Family: Ank (23)

Homo sapiens (Human) (14)

1a	Ank-3jueB01	B:639-671
1b	Ank-3jueB02	B:639-671
1c	Ank-3jueB03	B:639-671
1d	Ank-3jueB04	B:639-671

Clan: no clan defined [family: ArfGap] (6)

Family: ArfGap (6)

Homo sapiens (Human) (6)

2a	ArfGap-3jueB05	B:405-523
2b	ArfGap-3jueB06	B:405-523

Asymmetric Unit(hide GO term definitions)

Chain A,B (ACAP1_HUMAN | Q15027)

molecular function
	GO:0005096	GTPase activator activity	Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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).
biological process
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0055038	recycling endosome membrane	The lipid bilayer surrounding a recycling endosome.

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	ACAP1_HUMAN \| Q15027	:	3t9k 4ckg 4ckh 4f1p 4nsw

(no "Related Entries Specified in the PDB File" available for 3JUE)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 8)

Exons (0, 0)

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