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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN PROFILIN II

Authors :   I. M. Nodelman, G. D. Bowman, U. Lindberg, C. E. Schutt

Date :   17 Sep 99 (Deposition) - 22 Dec 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Acidic Profilin Isoform, Actin-Binding Protein, Poly-L- Proline Binding Protein, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. M. Nodelman, G. D. Bowman, U. Lindberg, C. E. Schutt
X-Ray Structure Determination Of Human Profilin Ii: A Comparative Structural Analysis Of Human Profilins.
J. Mol. Biol. V. 294 1271 1999
PubMed-ID: 10600384 | Reference-DOI: 10.1006/JMBI.1999.3318
(for further references see the PDB file header)

Molecule 1 - PROFILIN II
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3D
	Expression System Taxid	:	562
	Organ	:	BRAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	PG5	1	Ligand/Ion	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
2	PG6	1	Ligand/Ion	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
3	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:88 , ASN A:99 , HIS A:119 , GLY A:120 , ARG C:74	BINDING SITE FOR RESIDUE SO4 A 800
2	AC2	SOFTWARE	ARG B:88 , ASN B:99 , HIS B:119 , GLY B:120 , HOH B:206 , HOH B:561 , ARG D:74	BINDING SITE FOR RESIDUE SO4 B 801
3	AC3	SOFTWARE	HOH A:414 , ARG C:88 , ASN C:99 , HIS C:119 , GLY C:120 , HOH C:425	BINDING SITE FOR RESIDUE SO4 C 802
4	AC4	SOFTWARE	ARG B:74 , HOH B:574 , HOH B:577 , ASN D:99 , HIS D:119 , GLY D:120 , HOH D:575	BINDING SITE FOR RESIDUE SO4 D 803
5	AC5	SOFTWARE	SER C:5 , ASN C:9 , CYS C:12 , TYR C:133 , SER D:5 , ASN D:9	BINDING SITE FOR RESIDUE PG6 C 901
6	AC6	SOFTWARE	ASP C:26 , ALA C:27 , TYR C:29 , ASP D:26 , ALA D:27 , TYR D:29 , TRP D:31	BINDING SITE FOR RESIDUE PG5 D 902

(no "SS Bond" information available for 1D1J)

(no "Cis Peptide Bond" information available for 1D1J)

(no "SAP(SNP)/Variant" information available for 1D1J)

(no "PROSITE Motif" information available for 1D1J)

Asymmetric/Biological Unit (3, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3c	ENST00000239940	3c	ENSE00001881955	chr3:149688896-149688512	385	PROF2_HUMAN	1-44	44	4	A:1-43 B:2-43 C:1-43 D:1-43	43 42 43 43
1.5c	ENST00000239940	5c	ENSE00000779683	chr3:149686337-149686145	193	PROF2_HUMAN	45-109	65	4	A:44-108 B:44-108 C:44-108 D:44-108	65 65 65 65
1.6h	ENST00000239940	6h	ENSE00001008396	chr3:149684373-149682691	1683	PROF2_HUMAN	109-140	32	4	A:108-138 B:108-137 C:108-137 D:108-138	31 30 30 31

Asymmetric/Biological 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:138
 aligned with PROF2_HUMAN | P35080 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:138
                                    11        21        31        41        51        61        71        81        91       101       111       121       131        
          PROF2_HUMAN     2 AGWQSYVDNLMCDGCCQEAAIVGYCDAKYVWAATAGGVFQSITPIEIDMIVGKDREGFFTNGLTLGAKKCSVIRDSLYVDGDCTMDIRTKSQGGEPTYNVAVGRAGRVLVFVMGKEGVHGGGLNKKAYSMAKYLRDSG 139
               SCOP domains d1d1ja_ A: Profilin (actin-binding protein)                                                                                                SCOP domains
               CATH domains 1d1jA00 A:1-138 Dynein light chain 2a, cytoplasmic                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhh....eeeeeeee......eeee....hhhhhhhhhhhhhhh...hhhhhhheee..eeeeeeeee.......eeeeee.........eeeeee...eeeeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3c  PDB: A:1-43 UniProt: 1-44       Exon 1.5c  PDB: A:44-108 UniProt: 45-109                         ------------------------------ Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------Exon 1.6h  PDB: A:108-138       Transcript 1 (2)
                 1d1j A   1 AGWQSYVDNLMCDGCCQEAAIVGYCDAKYVWAATAGGVFQSITPIEIDMIVGKDREGFFTNGLTLGAKKCSVIRDSLYVDGDCTMDIRTKSQGGEPTYNVAVGRAGRALVIVMGKEGVHGGTLNKKAYELALYLRRSD 138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:136
 aligned with PROF2_HUMAN | P35080 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:136
                                    12        22        32        42        52        62        72        82        92       102       112       122       132      
          PROF2_HUMAN     3 GWQSYVDNLMCDGCCQEAAIVGYCDAKYVWAATAGGVFQSITPIEIDMIVGKDREGFFTNGLTLGAKKCSVIRDSLYVDGDCTMDIRTKSQGGEPTYNVAVGRAGRVLVFVMGKEGVHGGGLNKKAYSMAKYLRDS 138
               SCOP domains d1d1jb_ B: Profilin (actin-binding protein)                                                                                              SCOP domains
               CATH domains 1d1jB00 B:2-137 Dynein light chain 2a, cytoplasmic                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh....eeeeeeee......eeee...hhhhhhhhhhhhhhhh...hhhhhh.eee..eeeeeeeee.......eeeeee.........eeeeee...eeeeeee....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3c  PDB: B:2-43 UniProt: 1-44      Exon 1.5c  PDB: B:44-108 UniProt: 45-109                         ----------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------Exon 1.6h  PDB: B:108-137      Transcript 1 (2)
                 1d1j B   2 GWQSYVDNLMCDGCCQEAAIVGYCDAKYVWAATAGGVFQSITPIEIDMIVGKDREGFFTNGLTLGAKKCSVIRDSLYVDGDCTMDIRTKSQGGEPTYNVAVGRAGRALVIVMGKEGVHGGTLNKKAYELALYLRRS 137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131

Chain C from PDB  Type:PROTEIN  Length:137
 aligned with PROF2_HUMAN | P35080 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       
          PROF2_HUMAN     2 AGWQSYVDNLMCDGCCQEAAIVGYCDAKYVWAATAGGVFQSITPIEIDMIVGKDREGFFTNGLTLGAKKCSVIRDSLYVDGDCTMDIRTKSQGGEPTYNVAVGRAGRVLVFVMGKEGVHGGGLNKKAYSMAKYLRDS 138
               SCOP domains d1d1jc_ C: Profilin (actin-binding protein)                                                                                               SCOP domains
               CATH domains 1d1jC00 C:1-137 Dynein light chain 2a, cytoplasmic                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eeeeeeee......eeee....hhhhhhhhhhhhhhh...hhhhhhheee..eeeeeeeee.......eeeeee.........eeeeee...eeeeeee....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3c  PDB: C:1-43 UniProt: 1-44       Exon 1.5c  PDB: C:44-108 UniProt: 45-109                         ----------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------Exon 1.6h  PDB: C:108-137      Transcript 1 (2)
                 1d1j C   1 AGWQSYVDNLMCDGCCQEAAIVGYCDAKYVWAATAGGVFQSITPIEIDMIVGKDREGFFTNGLTLGAKKCSVIRDSLYVDGDCTMDIRTKSQGGEPTYNVAVGRAGRALVIVMGKEGVHGGTLNKKAYELALYLRRS 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain D from PDB  Type:PROTEIN  Length:138
 aligned with PROF2_HUMAN | P35080 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:138
                                    11        21        31        41        51        61        71        81        91       101       111       121       131        
          PROF2_HUMAN     2 AGWQSYVDNLMCDGCCQEAAIVGYCDAKYVWAATAGGVFQSITPIEIDMIVGKDREGFFTNGLTLGAKKCSVIRDSLYVDGDCTMDIRTKSQGGEPTYNVAVGRAGRVLVFVMGKEGVHGGGLNKKAYSMAKYLRDSG 139
               SCOP domains d1d1jd_ D: Profilin (actin-binding protein)                                                                                                SCOP domains
               CATH domains 1d1jD00 D:1-138 Dynein light chain 2a, cytoplasmic                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eeeeeeee......eeee....hhhhhhhhhhhhhhh...hhhhhhheee..eeeeeeeee.......eeeeee.........eeeeee...eeeeeee....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3c  PDB: D:1-43 UniProt: 1-44       Exon 1.5c  PDB: D:44-108 UniProt: 45-109                         ------------------------------ Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------Exon 1.6h  PDB: D:108-138       Transcript 1 (2)
                 1d1j D   1 AGWQSYVDNLMCDGCCQEAAIVGYCDAKYVWAATAGGVFQSITPIEIDMIVGKDREGFFTNGLTLGAKKCSVIRDSLYVDGDCTMDIRTKSQGGEPTYNVAVGRAGRALVIVMGKEGVHGGTLNKKAYELALYLRRSD 138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Profilin-like (304)

Superfamily: Profilin (actin-binding protein) (31)

Family: Profilin (actin-binding protein) (29)

Protein domain: Profilin (actin-binding protein) (23)

Human (Homo sapiens), isoform II [TaxId: 9606] (1)

1a	d1d1ja_	A:
1b	d1d1jb_	B:
1c	d1d1jc_	C:
1d	d1d1jd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Beta-Lactamase (202)

Homologous Superfamily: Dynein light chain 2a, cytoplasmic (37)

Human (Homo sapiens) (11)

1a	1d1jB00	B:2-137
1b	1d1jC00	C:1-137
1c	1d1jA00	A:1-138
1d	1d1jD00	D:1-138

(no "Pfam Domain" information available for 1D1J)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (PROF2_HUMAN | P35080)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0003785	actin monomer binding	Interacting selectively and non-covalently with monomeric actin, also known as G-actin.
	GO:0000774	adenyl-nucleotide exchange factor activity	Stimulates the hydrolysis and exchange of adenyl nucleotides by other proteins.
	GO:0005546	phosphatidylinositol-4,5-bisphosphate binding	Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions.
	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: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:0030837	negative regulation of actin filament polymerization	Any process that stops, prevents, or reduces the frequency, rate or extent of actin polymerization.
	GO:0010633	negative regulation of epithelial cell migration	Any process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell migration.
	GO:1900028	negative regulation of ruffle assembly	Any process that stops, prevents or reduces the frequency, rate or extent of ruffle assembly.
	GO:0032781	positive regulation of ATPase activity	Any process that activates or increases the rate of ATP hydrolysis by an ATPase.
	GO:0032233	positive regulation of actin filament bundle assembly	Any process that activates or increases the frequency, rate or extent of the assembly of actin filament bundles.
	GO:0030838	positive regulation of actin filament polymerization	Any process that activates or increases the frequency, rate or extent of actin polymerization.
	GO:0033138	positive regulation of peptidyl-serine phosphorylation	Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine.
	GO:0051496	positive regulation of stress fiber assembly	Any process that activates or increases the frequency, rate or extent of the assembly of a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts.
	GO:0050821	protein stabilization	Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
	GO:0030833	regulation of actin filament polymerization	Any process that modulates the frequency, rate or extent of the assembly of actin filaments by the addition of actin monomers to a filament.
	GO:2000300	regulation of synaptic vesicle exocytosis	Any process that modulates the frequency, rate or extent of synaptic vesicle exocytosis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	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:0043195	terminal bouton	Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it.

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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