2ZHJ - JenaLib

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Title :   CRYSTAL STRUCTURE ANALYSIS OF THE SODIUM-BOUND ANNEXIN A4 AT 1.34 A RESOLUTION

Authors :   K. Butsushita, K. Ida, S. -I. Fukuoka, Y. Arii

Date :   06 Feb 08 (Deposition) - 10 Feb 09 (Release) - 10 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.35

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

Keywords :   Zynogen Granule, Membrane Binding Protein, Metal Binding Protein, Annexin, Calcium, Calcium/Phospholipid-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Butsushita, K. Inoue, K. Ida, S. -I. Fukuoka, Y. Arii
Structural Analysis For The Soduim-Dependent Dissociation Of Annexin A4: Crystal Structures Of Soduim-Bound Annexin A4 At High Resolutions
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - ANNEXIN A4
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX3X
	Expression System Strain	:	HB101
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ANXA4
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:99 , GLY A:101 , GLY A:103 , ASP A:143	BINDING SITE FOR RESIDUE NA A 320
2	AC2	SOFTWARE	GLY A:182 , ARG A:185 , GLY A:187 , GLU A:227 , HOH A:416 , HOH A:440	BINDING SITE FOR RESIDUE NA A 321

(no "SS Bond" information available for 2ZHJ)

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ANNEXIN	PS00223	Annexins repeated domain signature.	ANXA4_RAT	31-83 103-155 187-239 262-314	4	A:31-83 A:103-155 A:187-239 A:262-314

Biological Unit 1 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ANNEXIN	PS00223	Annexins repeated domain signature.	ANXA4_RAT	31-83 103-155 187-239 262-314	8	A:31-83 A:103-155 A:187-239 A:262-314

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ANNEXIN	PS00223	Annexins repeated domain signature.	ANXA4_RAT	31-83 103-155 187-239 262-314	4	A:31-83 A:103-155 A:187-239 A:262-314

(no "Exon" information available for 2ZHJ)

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:315
 aligned with ANXA4_RAT | P55260 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:315
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311     
            ANXA4_RAT     2 ETKGGTVKAASGFNATEDAQVLRKAMKGLGTDEDAIIGVLACRNTAQRQEIRTAYKSTIGRDLLEDLKSELSSNFEQVILGMMTPTVLYDVQELRRAMKGAGTDEGCLIEILASRNPEEIRRINQTYQQQYGRSLEEDICSDTSFMFQRVLVSLTAGGRDEGNYLDDALVRQDAQDLYEAGEKRWGTDEVKFLSILCSRNRNHLLHVFDEYKRISQKDIEQSIKSETSGSFEDALLAIVKCMRNKPAYFAERLYKSMKGLGTDDSTLIRVMVSRAEIDMLDIPANFKRVYGKSLYSFIKGDTSGDYRKVLLILCG 316
               SCOP domains d2zhja_ A: automated matches                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains -----------2zhjA01 A:13-85  [code=1.10.220.10, no name defined]                     2zhjA02 A:86-159  [code=1.10.220.10, no name defined]                     2zhjA03 A:160-245  [code=1.10.220.10, no name defined]                                2zhjA04 A:246-316  [code=1.10.220.10, no name defined]                  CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Annexin-2zhjA01 A:249-314                                         -- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Annexin-2zhjA02 A:249-314                                         -- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Annexin-2zhjA03 A:249-314                                         -- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Annexin-2zhjA04 A:249-314                                         -- Pfam domains (4)
         Sec.struct. author .............hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------ANNEXIN  PDB: A:31-83 UniProt: 31-83                 -------------------ANNEXIN  PDB: A:103-155 UniProt: 103-155             -------------------------------ANNEXIN  PDB: A:187-239 UniProt: 187-239             ----------------------ANNEXIN  PDB: A:262-314 UniProt: 262-314             -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zhj A   2 ETKGGTVKAASGFNATEDAQVLRKAMKGLGTDEDAIIGVLACRNTAQRQEIRTAYKSTIGRDLLEDLKSELSSNFEQVILGMMTPTVLYDVQELRRAMKGAGTDEGCLIEILASRNPEEIRRINQTYQQQYGRSLEEDICSDTSFMFQRVLVSLTAGGRDEGNYLDDALVKQDAQDLYEAGEKRWGTDEVKFLSILCSRNRNHLLHVFDEYKRISQKDIEQSIKSETSGSFEDALLAIVKCMRNKPAYFAERLYKSMKGLGTDDSTLIRVMVSRAEIDMLDIRANFKRLYGKSLYSFIKGDTSGDYRKVLLILCG 316
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311

Chain A from PDB  Type:PROTEIN  Length:315
 aligned with Q5U362_RAT | Q5U362 from UniProtKB/TrEMBL  Length:319

    Alignment length:315
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311     
           Q5U362_RAT     2 ETKGGTVKAASGFNATEDAQVLRKAMKGLGTDEDAIIGVLACRNTAQRQEIRTAYKSTIGRDLLEDLKSELSSNFEQVILGMMTPTVLYDVQELRRAMKGAGTDEGCLIEILASRNPEEIRRINQTYQQQYGRSLEEDICSDTSFMFQRVLVSLTAGGRDEGNYLDDALVKQDAQDLYEAGEKRWGTDEVKFLSILCSRNRNHLLHVFDEYKRISQKDIEQSIKSETSGSFEDALLAIVKCMRNKPAYFAERLYKSMKGLGTDDSTLIRVMVSRAEIDMLDIRANFKRLYGKSLYSFIKGDTSGDYRKVLLILCG 316
               SCOP domains d2zhja_ A: automated matches                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains -----------2zhjA01 A:13-85  [code=1.10.220.10, no name defined]                     2zhjA02 A:86-159  [code=1.10.220.10, no name defined]                     2zhjA03 A:160-245  [code=1.10.220.10, no name defined]                                2zhjA04 A:246-316  [code=1.10.220.10, no name defined]                  CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Annexin-2zhjA01 A:249-314                                         -- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Annexin-2zhjA02 A:249-314                                         -- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Annexin-2zhjA03 A:249-314                                         -- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Annexin-2zhjA04 A:249-314                                         -- Pfam domains (4)
         Sec.struct. author .............hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zhj A   2 ETKGGTVKAASGFNATEDAQVLRKAMKGLGTDEDAIIGVLACRNTAQRQEIRTAYKSTIGRDLLEDLKSELSSNFEQVILGMMTPTVLYDVQELRRAMKGAGTDEGCLIEILASRNPEEIRRINQTYQQQYGRSLEEDICSDTSFMFQRVLVSLTAGGRDEGNYLDDALVKQDAQDLYEAGEKRWGTDEVKFLSILCSRNRNHLLHVFDEYKRISQKDIEQSIKSETSGSFEDALLAIVKCMRNKPAYFAERLYKSMKGLGTDDSTLIRVMVSRAEIDMLDIRANFKRLYGKSLYSFIKGDTSGDYRKVLLILCG 316
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311

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: All alpha proteins (14657)

Fold: Annexin (61)

Superfamily: Annexin (61)

Family: Annexin (56)

Protein domain: automated matches (6)

Norway rat (Rattus norvegicus) [TaxId: 10116] (2)

d2zhja_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Annexin V; domain 1 (80)

Homologous Superfamily: [code=1.10.220.10, no name defined] (58)

Rat (Rattus norvegicus) (2)

1a	2zhjA02	A:86-159
1b	2zhjA01	A:13-85
1c	2zhjA04	A:246-316
1d	2zhjA03	A:160-245

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Annexin] (14)

Family: Annexin (14)

Rattus norvegicus (Rat) (4)

1a	Annexin-2zhjA01	A:249-314
1b	Annexin-2zhjA02	A:249-314
1c	Annexin-2zhjA03	A:249-314
1d	Annexin-2zhjA04	A:249-314

Asymmetric Unit(hide GO term definitions)

Chain A (Q5U362_RAT | Q5U362)

molecular function
	GO:0051059	NF-kappaB binding	Interacting selectively and non-covalently with NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0005544	calcium-dependent phospholipid binding	Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester, in the presence of calcium.
	GO:0048306	calcium-dependent 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), in the presence of calcium.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
biological process
	GO:0007219	Notch signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0030855	epithelial cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
	GO:0032088	negative regulation of NF-kappaB transcription factor activity	Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB.
	GO:2000483	negative regulation of interleukin-8 secretion	Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-8 secretion.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	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:0031965	nuclear membrane	Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	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.
	GO:0012506	vesicle membrane	The lipid bilayer surrounding any membrane-bounded vesicle in the cell.

Chain A (ANXA4_RAT | P55260)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0005544	calcium-dependent phospholipid binding	Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester, in the presence of calcium.
biological process
	GO:0006887	exocytosis	A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.

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	Q5U362_RAT \| Q5U362
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	ANXA4_RAT \| P55260	:	2zhi
	Q5U362_RAT \| Q5U362	:	2zhi

1ann	CALCIUM-BOUND FORM OF THE SAME PROTEIN
1aow	APO FORM OF THE SAME PROTEIN
1i4a	CALCIUM-BOUND FORM OF THE SAME PROTEIN
2zhi

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