User:Alice Harmon/EF Hand: Difference between revisions

Line 9:

{|

|Residue

|Residue:

|D-x-[DNS]-{ILVFYW}-[DENSTG]-[DNQGHRK]-{GP}-[LIVMC]-[DENQSTAGC]- x(2) -[DE]

|-

|Position

|Position:

|1-2---3------4xxxx----5---------6------7-----8---------9-------10,11---12

|}

where x indicates any residue; any residue in square brackets [ ] is possible at that position; none of the residues in curly brackets { } are possible: and x(2) indicates a series of two x's.

The calcium ion is coordinated by seven oxygen atoms that form a pentagonal bipyramid ~~(five atoms form the base of the pyramid and~~ the ~~other two~~ the ~~points)~~. One oxygen is contributed by each of the side chains of residues in positions 1, 3, 5, 9; two are from the side chain of E or D at position 12; one is from the backbone of the residue at position 7; and one from water.

[[Image:Pyramid small.jpg|right]]

The calcium ion is coordinated by seven oxygen atoms that form a pentagonal bipyramid as shown in the figure to the right. One oxygen is contributed by each of the side chains of residues in positions 1, 3, 5, and 7 of the motif; two are from the side chain of E or D at position 12; one is from the backbone of the residue at position 7; and one from water. Labels in the figure indicate the arrangement of the oxygen atoms in the structure. The 3D structure is depicted in the scenes below.

~~Below are~~ three examples of EF-hand proteins. [[parvalbumin]] is a monomeric protein that has a pair of EF-hands, [[calmodulin]] is a monomer with two pair, and [[calcium-dependent protein kinase]] is a monomer with a protein kinase catalytic domain (gold) and calcium-binding domain (blue) that has two pair of EF hands. As shown in these examples EF-hands often occur in pairs, which enables the cooperative binding of calcium ions. The initial scene shows the proteins in cartoon with Ca2+ in green space fill. The calcium binding domain of CDPK is blue and the kinase catalytic domain is in gold and has an ATP analog (sticks in CPK colors) bound in its active site.

The 3D structure of EF-hands is depicted in the scenes below, which show three examples of EF-hand proteins. [[parvalbumin]] is a monomeric protein that has a pair of EF-hands, [[calmodulin]] is a monomer with two pair, and [[calcium-dependent protein kinase]] is a monomer with a protein kinase catalytic domain (gold) and calcium-binding domain (blue) that has two pair of EF hands. As shown in these examples EF-hands often occur in pairs, which enables the cooperative binding of calcium ions. The initial scene shows the proteins in cartoon with Ca2+ in green space fill. The calcium binding domain of CDPK is blue and the kinase catalytic domain is in gold and has an ATP analog (sticks in CPK colors) bound in its active site.

Scenes numbered 1 show pairs of EF-hands in each protein, one in blue and one in gold, which are linked by the sequence shown in orchid.

Scenes numbered 1 are the default scenes showing the holoproteins.

Scenes numbered 2 isolate one EF-hand: the eponymous EF-hand of parvalbumen, EF-hand I (they are numbered I-IV) in calmodulin, and EF-hand IV of CDPK.

Scenes numbered 2 show pairs of EF-hands in each protein, one in blue and one in gold, which are linked by the sequence shown in orchid.

Scenes numbered 3 show the calcium binding loops, which are shown in the same orientation. The five oxygen atoms that form the the base of the bipyramid are contributed by four residues (positions 3, 5, 9, and 12) distributed around the equator of the calcium ion, one pyramid point ("north in the scenes) is the oxygen from water, and the "south" point is the invariant D at position 1 in the motif.

Scenes numbered 3 isolate one EF-hand: the eponymous EF-hand of parvalbumen, EF-hand I (they are numbered I-IV) in calmodulin, and EF-hand IV of CDPK.

Scenes numbered 4 show the calcium binding loops, which are shown in the same orientation. The five oxygen atoms that form the the base of the bipyramid are contributed by four residues (positions 3, 5, 9, and 12) distributed around the equator of the calcium ion, one pyramid point ("north in the scenes) is the oxygen from water, and the "south" point is the invariant D at position 1 in the motif.

{|

| <applet load='4cpv' size='300' frame='true' align='right' caption='4cpv - Carp parvalbumin' scene='56/562354/Parvalbumin/1' /> '''4cpv''' <scene name='56/562354/Parvalbumin/2'>1. Pair of EF-hands</scene> <scene name='56/562354/Parvalbumin/3'>2. The original EF-Hand</scene> <scene name='56/562354/Parvalbumin/6'>3. Calcium-binding loop</scene>

| <applet load='4cpv' size='300' frame='true' align='right' caption='4cpv - Carp parvalbumin' scene='56/562354/Parvalbumin/1' /> '''4cpv''' <scene name='56/562354/Parvalbumin/1'>1. Holoprotein</scene> <scene name='56/562354/Parvalbumin/2'>2. Pair of EF-hands</scene> <scene name='56/562354/Parvalbumin/3'>3. The original EF-Hand</scene> <scene name='56/562354/Parvalbumin/6'>4. Calcium-binding loop</scene>

| <applet load='1prw' size='300' frame='true' align='right' caption='1prw - Bovine calmodulin' scene='56/562354/Calmodulin/1' /> '''1prw''' <scene name='56/562354/Calmodulin/3'>1. Pair of EF-hands</scene> <scene name='56/562354/Calmodulin/4'>2. EF-hand I</scene> <scene name='56/562354/Calmodulin/7'>3. Calcium-binding loop</scene>

| <applet load='1prw' size='300' frame='true' align='right' caption='1prw - Bovine calmodulin' scene='56/562354/Calmodulin/1' /> '''1prw''' <scene name='56/562354/Calmodulin/1'>1. Holoprotein</scene> <scene name='56/562354/Calmodulin/3'>2. Pair of EF-hands</scene> <scene name='56/562354/Calmodulin/3'>2. EF-hand I</scene> <scene name='56/562354/Calmodulin/7'>4. Calcium-binding loop</scene>

| <applet load='3HX4' size='300' frame='true' align='left' caption='3hx4 - active TgCDPK1' scene = '56/562354/Cdpk/1' /> '''3HX4''' <scene name='56/562354/Cdpk_ef_hand_pair/2'>1. Pair of EF-hands</scene> <scene name='56/562354/Cdpk_ef_iv/1'>2. EF-hand IV</scene> <scene name='56/562354/Cdpk_ef_iv/3'>3. Calcium-binding loop</scene>

| <applet load='3HX4' size='300' frame='true' align='left' caption='3hx4 - active TgCDPK1' scene = '56/562354/Cdpk/1' /> '''3HX4''' <scene name='56/562354/Cdpk/1'>1. Holoprotein</scene> <scene name='56/562354/Cdpk_ef_hand_pair/2'>2. Pair of EF-hands</scene> <scene name='56/562354/Cdpk_ef_iv/1'>3. EF-hand IV</scene> <scene name='56/562354/Cdpk_ef_iv/3'>4. Calcium-binding loop</scene>

|}

@@ Line 9: / Line 9: @@
 {|
-|Residue
+|Residue:
 |<font face = courier>D-x-[DNS]-{ILVFYW}-[DENSTG]-[DNQGHRK]-{GP}-[LIVMC]-[DENQSTAGC]- x(2) -[DE]</font><br>
 |-
-|Position
+|Position:
 |<font face =courier>1-2-<font color='white'>--</font>3<font color='white'>--</font>-<font color='white'>---</font>4<font color='white'>xxxx</font>-<font color='white'>---</font>5<font color='white'>----</font>-<font color='white'>----</font>6<font color='white'>----</font>-<font color='white'>-</font>7<font color='white'>--</font>-<font color='white'>--</font>8<font color='white'>----</font>-<font color='white'>----</font>9<font color='white'>------</font>-10,11<font color='white'>-</font>-<font color='white'>-</font>12
 |}
 where x indicates any residue; any residue in square brackets [ ] is possible at that position; none of the residues in curly brackets { } are possible: and x(2) indicates a series of two x's.
-The calcium ion is coordinated by seven oxygen atoms that form a pentagonal bipyramid (five atoms form the base of the pyramid and the other two the points). One oxygen is contributed by each of the side chains of residues in positions 1, 3, 5, 9; two are from the side chain of E or D at position 12; one is from the backbone of the residue at position 7; and one from water.
+[[Image:Pyramid small.jpg|right]]
+The calcium ion is coordinated by seven oxygen atoms that form a pentagonal bipyramid as shown in the figure to the right. One oxygen is contributed by each of the side chains of residues in positions 1, 3, 5, and 7 of the motif; two are from the side chain of E or D at position 12; one is from the backbone of the residue at position 7; and one from water. Labels in the figure indicate the arrangement of the oxygen atoms in the structure. The 3D structure is depicted in the scenes below.
-Below are three examples of EF-hand proteins. [[parvalbumin]] is a monomeric protein that has a pair of EF-hands, [[calmodulin]] is a monomer with two pair, and [[calcium-dependent protein kinase]] is a monomer with a protein kinase catalytic domain (gold) and calcium-binding domain (blue) that has two pair of EF hands. As shown in these examples EF-hands often occur in pairs, which enables the cooperative binding of calcium ions. The initial scene shows the proteins in cartoon with Ca2+ in green space fill. The calcium binding domain of CDPK is blue and the kinase catalytic domain is in gold and has an ATP analog (sticks in CPK colors) bound in its active site.
+The 3D structure of EF-hands is depicted in the scenes below, which show three examples of EF-hand proteins. [[parvalbumin]] is a monomeric protein that has a pair of EF-hands, [[calmodulin]] is a monomer with two pair, and [[calcium-dependent protein kinase]] is a monomer with a protein kinase catalytic domain (gold) and calcium-binding domain (blue) that has two pair of EF hands. As shown in these examples EF-hands often occur in pairs, which enables the cooperative binding of calcium ions. The initial scene shows the proteins in cartoon with Ca2+ in green space fill. The calcium binding domain of CDPK is blue and the kinase catalytic domain is in gold and has an ATP analog (sticks in CPK colors) bound in its active site.
-Scenes numbered 1 show pairs of EF-hands in each protein, one in blue and one in gold, which are linked by the sequence shown in orchid.<br>
+Scenes numbered 1 are the default scenes showing the holoproteins. <br>
-Scenes numbered 2 isolate one EF-hand: the eponymous EF-hand of parvalbumen, EF-hand I (they are numbered I-IV) in calmodulin, and EF-hand IV of CDPK.<br>
+Scenes numbered 2 show pairs of EF-hands in each protein, one in blue and one in gold, which are linked by the sequence shown in orchid.<br>
-Scenes numbered 3 show the calcium binding loops, which are shown in the same orientation. The five oxygen atoms that form the the base of the bipyramid are contributed by four residues (positions 3, 5, 9, and 12) distributed around the equator of the calcium ion, one pyramid point ("north in the scenes) is the oxygen from water, and the "south" point is the invariant D at position 1 in the motif.
+Scenes numbered 3 isolate one EF-hand: the eponymous EF-hand of parvalbumen, EF-hand I (they are numbered I-IV) in calmodulin, and EF-hand IV of CDPK.<br>
+Scenes numbered 4 show the calcium binding loops, which are shown in the same orientation. The five oxygen atoms that form the the base of the bipyramid are contributed by four residues (positions 3, 5, 9, and 12) distributed around the equator of the calcium ion, one pyramid point ("north in the scenes) is the oxygen from water, and the "south" point is the invariant D at position 1 in the motif.
 {|
-| <applet load='4cpv' size='300' frame='true' align='right' caption='4cpv - Carp parvalbumin' scene='56/562354/Parvalbumin/1' /><Br>'''4cpv''' <Br><scene name='56/562354/Parvalbumin/2'>1. Pair of EF-hands</scene><br><scene name='56/562354/Parvalbumin/3'>2. The original EF-Hand</scene><br><scene name='56/562354/Parvalbumin/6'>3. Calcium-binding loop</scene>
+| <applet load='4cpv' size='300' frame='true' align='right' caption='4cpv - Carp parvalbumin' scene='56/562354/Parvalbumin/1' /><Br>'''4cpv''' <Br><scene name='56/562354/Parvalbumin/1'>1. Holoprotein</scene><Br><scene name='56/562354/Parvalbumin/2'>2. Pair of EF-hands</scene><br><scene name='56/562354/Parvalbumin/3'>3. The original EF-Hand</scene><br><scene name='56/562354/Parvalbumin/6'>4. Calcium-binding loop</scene>
-| <applet load='1prw' size='300' frame='true' align='right' caption='1prw - Bovine calmodulin' scene='56/562354/Calmodulin/1' /><Br>'''1prw''' <Br><scene name='56/562354/Calmodulin/3'>1. Pair of EF-hands</scene><br><scene name='56/562354/Calmodulin/4'>2. EF-hand I</scene><br><scene name='56/562354/Calmodulin/7'>3. Calcium-binding loop</scene>
+| <applet load='1prw' size='300' frame='true' align='right' caption='1prw - Bovine calmodulin' scene='56/562354/Calmodulin/1' /><Br>'''1prw''' <Br><scene name='56/562354/Calmodulin/1'>1. Holoprotein</scene><Br><scene name='56/562354/Calmodulin/3'>2. Pair of EF-hands</scene><br><scene name='56/562354/Calmodulin/3'>2. EF-hand I</scene><br><scene name='56/562354/Calmodulin/7'>4. Calcium-binding loop</scene>
-| <applet load='3HX4' size='300' frame='true' align='left' caption='3hx4 - active TgCDPK1' scene = '56/562354/Cdpk/1' /><Br>'''3HX4'''<Br><scene name='56/562354/Cdpk_ef_hand_pair/2'>1. Pair of EF-hands</scene><br><scene name='56/562354/Cdpk_ef_iv/1'>2. EF-hand IV</scene><br><scene name='56/562354/Cdpk_ef_iv/3'>3. Calcium-binding loop</scene>
+| <applet load='3HX4' size='300' frame='true' align='left' caption='3hx4 - active TgCDPK1' scene = '56/562354/Cdpk/1' /><Br>'''3HX4'''<Br><scene name='56/562354/Cdpk/1'>1. Holoprotein</scene><Br><scene name='56/562354/Cdpk_ef_hand_pair/2'>2. Pair of EF-hands</scene><br><scene name='56/562354/Cdpk_ef_iv/1'>3. EF-hand IV</scene><br><scene name='56/562354/Cdpk_ef_iv/3'>4. Calcium-binding loop</scene>
 |}