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- PDB-4fao: Specificity and Structure of a high affinity Activin-like 1 (ALK1... -

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Basic information

Entry
Database: PDB / ID: 4fao
TitleSpecificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex
Components
  • Activin receptor type-2B
  • Growth/differentiation factor 2
  • Serine/threonine-protein kinase receptor R3
KeywordsSIGNALING PROTEIN/SIGNALING PROTEIN / tgf-beta / CTK / cystine knot / extracellular domain / receptor / SIGNALING PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


Regulation of signaling by NODAL / activin receptor activity / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / regulation of endothelial cell proliferation / dorsal aorta morphogenesis / blood vessel maturation / negative regulation of endothelial cell differentiation / positive regulation of epithelial cell differentiation / venous blood vessel development ...Regulation of signaling by NODAL / activin receptor activity / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / regulation of endothelial cell proliferation / dorsal aorta morphogenesis / blood vessel maturation / negative regulation of endothelial cell differentiation / positive regulation of epithelial cell differentiation / venous blood vessel development / positive regulation of cartilage development / positive regulation of chondrocyte differentiation / transforming growth factor beta receptor activity / lymphangiogenesis / trophoblast cell migration / BMP receptor complex / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / retina vasculature development in camera-type eye / positive regulation of endothelial cell differentiation / embryonic foregut morphogenesis / negative regulation of focal adhesion assembly / regulation of blood vessel endothelial cell migration / endothelial tube morphogenesis / activin receptor complex / artery development / transforming growth factor beta receptor activity, type I / activin receptor activity, type I / activin receptor activity, type II / BMP receptor activity / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / transforming growth factor beta receptor activity, type II / transforming growth factor beta receptor activity, type III / activin binding / pattern specification process / cellular response to BMP stimulus / Signaling by BMP / negative regulation of cell adhesion / Signaling by Activin / activin receptor signaling pathway / positive regulation of BMP signaling pathway / positive regulation of bicellular tight junction assembly / Signaling by NODAL / gastrulation with mouth forming second / dorsal/ventral pattern formation / transforming growth factor beta binding / pancreas development / kinase activator activity / determination of left/right symmetry / negative regulation of ossification / wound healing, spreading of epidermal cells / blood vessel morphogenesis / insulin secretion / negative regulation of endothelial cell migration / negative regulation of cold-induced thermogenesis / blood circulation / anterior/posterior pattern specification / skeletal system morphogenesis / cartilage development / cell surface receptor protein serine/threonine kinase signaling pathway / endocardial cushion morphogenesis / organ growth / branching involved in blood vessel morphogenesis / positive regulation of Notch signaling pathway / growth factor binding / negative regulation of DNA replication / SMAD binding / negative regulation of endothelial cell proliferation / mesoderm development / odontogenesis of dentin-containing tooth / roof of mouth development / regulation of DNA replication / negative regulation of blood vessel endothelial cell migration / positive regulation of SMAD protein signal transduction / blood vessel remodeling / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / vasculogenesis / response to glucose / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / protein serine/threonine/tyrosine kinase activity / transforming growth factor beta receptor signaling pathway / ossification / negative regulation of angiogenesis / protein serine/threonine kinase activator activity / negative regulation of cell migration / post-embryonic development / cytokine activity / kidney development / positive regulation of interleukin-8 production / growth factor activity / lung development / negative regulation of cell growth / cellular response to growth factor stimulus / regulation of blood pressure / positive regulation of angiogenesis / osteoblast differentiation / heart development
Similarity search - Function
GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor beta, conserved site / TGF-beta family signature. ...GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / Snake toxin-like superfamily / Ribbon / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Activin receptor type-1-like / Activin receptor type-2B / Growth/differentiation factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.357 Å
AuthorsTownson, S.A. / Martinez-Hackert, E. / Greppi, C. / Lowden, P. / Sako, D. / Liu, J. / Ucran, J.A. / Liharska, K. / Underwood, K.W. / Seehra, J. ...Townson, S.A. / Martinez-Hackert, E. / Greppi, C. / Lowden, P. / Sako, D. / Liu, J. / Ucran, J.A. / Liharska, K. / Underwood, K.W. / Seehra, J. / Kumar, R. / Grinberg, A.V.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Specificity and Structure of a High Affinity Activin Receptor-like Kinase 1 (ALK1) Signaling Complex.
Authors: Townson, S.A. / Martinez-Hackert, E. / Greppi, C. / Lowden, P. / Sako, D. / Liu, J. / Ucran, J.A. / Liharska, K. / Underwood, K.W. / Seehra, J. / Kumar, R. / Grinberg, A.V.
History
DepositionMay 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Aug 29, 2012Group: Database references
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Growth/differentiation factor 2
B: Growth/differentiation factor 2
C: Serine/threonine-protein kinase receptor R3
D: Serine/threonine-protein kinase receptor R3
E: Activin receptor type-2B
F: Activin receptor type-2B
G: Growth/differentiation factor 2
H: Growth/differentiation factor 2
I: Serine/threonine-protein kinase receptor R3
J: Serine/threonine-protein kinase receptor R3
K: Activin receptor type-2B
L: Activin receptor type-2B
M: Growth/differentiation factor 2
N: Growth/differentiation factor 2
O: Serine/threonine-protein kinase receptor R3
P: Serine/threonine-protein kinase receptor R3
Q: Activin receptor type-2B
R: Activin receptor type-2B
S: Growth/differentiation factor 2
T: Growth/differentiation factor 2
U: Serine/threonine-protein kinase receptor R3
V: Serine/threonine-protein kinase receptor R3
W: Activin receptor type-2B
X: Activin receptor type-2B
a: Growth/differentiation factor 2
b: Growth/differentiation factor 2
c: Serine/threonine-protein kinase receptor R3
d: Serine/threonine-protein kinase receptor R3
e: Activin receptor type-2B
f: Activin receptor type-2B
g: Growth/differentiation factor 2
h: Growth/differentiation factor 2
i: Serine/threonine-protein kinase receptor R3
j: Serine/threonine-protein kinase receptor R3
k: Activin receptor type-2B
l: Activin receptor type-2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)459,21666
Polymers453,76936
Non-polymers5,44730
Water00
1
A: Growth/differentiation factor 2
B: Growth/differentiation factor 2
C: Serine/threonine-protein kinase receptor R3
D: Serine/threonine-protein kinase receptor R3
E: Activin receptor type-2B
F: Activin receptor type-2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,53611
Polymers75,6286
Non-polymers9085
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11580 Å2
ΔGint-62 kcal/mol
Surface area26500 Å2
MethodPISA
2
G: Growth/differentiation factor 2
H: Growth/differentiation factor 2
I: Serine/threonine-protein kinase receptor R3
J: Serine/threonine-protein kinase receptor R3
K: Activin receptor type-2B
L: Activin receptor type-2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,53611
Polymers75,6286
Non-polymers9085
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11390 Å2
ΔGint-64 kcal/mol
Surface area26330 Å2
MethodPISA
3
M: Growth/differentiation factor 2
N: Growth/differentiation factor 2
O: Serine/threonine-protein kinase receptor R3
P: Serine/threonine-protein kinase receptor R3
Q: Activin receptor type-2B
R: Activin receptor type-2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,53611
Polymers75,6286
Non-polymers9085
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11280 Å2
ΔGint-65 kcal/mol
Surface area26390 Å2
MethodPISA
4
S: Growth/differentiation factor 2
T: Growth/differentiation factor 2
U: Serine/threonine-protein kinase receptor R3
V: Serine/threonine-protein kinase receptor R3
W: Activin receptor type-2B
X: Activin receptor type-2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,53611
Polymers75,6286
Non-polymers9085
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11310 Å2
ΔGint-61 kcal/mol
Surface area26440 Å2
MethodPISA
5
a: Growth/differentiation factor 2
b: Growth/differentiation factor 2
c: Serine/threonine-protein kinase receptor R3
d: Serine/threonine-protein kinase receptor R3
e: Activin receptor type-2B
f: Activin receptor type-2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,53611
Polymers75,6286
Non-polymers9085
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11490 Å2
ΔGint-63 kcal/mol
Surface area26390 Å2
MethodPISA
6
g: Growth/differentiation factor 2
h: Growth/differentiation factor 2
i: Serine/threonine-protein kinase receptor R3
j: Serine/threonine-protein kinase receptor R3
k: Activin receptor type-2B
l: Activin receptor type-2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,53611
Polymers75,6286
Non-polymers9085
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11550 Å2
ΔGint-64 kcal/mol
Surface area26190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.453, 216.453, 216.953
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31G
41H
51M
61N
71S
81T
91a
101b
111g
121h
12E
22X
32e
42f
52k
62l
72W
82F
92K
102L
112Q
122R
13C
23U
33V
43c
53d
63i
73j
83P
93D
103I
113J
123O

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN A AND (RESSEQ 8:110 )A8 - 110
211CHAIN B AND (RESSEQ 8:110 )B8 - 110
311CHAIN G AND (RESSEQ 8:110 )G8 - 110
411CHAIN H AND (RESSEQ 8:110 )H8 - 110
511CHAIN M AND (RESSEQ 8:110 )M8 - 110
611CHAIN N AND (RESSEQ 8:110 )N8 - 110
711CHAIN S AND (RESSEQ 8:110 )S8 - 110
811CHAIN T AND (RESSEQ 8:110 )T8 - 110
911CHAIN a AND (RESSEQ 8:110 )a8 - 110
1011CHAIN b AND (RESSEQ 8:110 )b8 - 110
1111CHAIN g AND (RESSEQ 8:110 )g8 - 110
1211CHAIN h AND (RESSEQ 8:110 )h8 - 110
112CHAIN E AND (RESSEQ 8:99 )E8 - 99
212CHAIN X AND (RESSEQ 8:99 )X8 - 99
312CHAIN e AND (RESSEQ 8:99 )e8 - 99
412CHAIN f AND (RESSEQ 8:99 )f8 - 99
512CHAIN k AND (RESSEQ 8:99 )k8 - 99
612CHAIN l AND (RESSEQ 8:99 )l8 - 99
712CHAIN W AND (RESSEQ 8:99 )W8 - 99
812CHAIN F AND (RESSEQ 8:99 )F8 - 99
912CHAIN K AND (RESSEQ 8:99 )K8 - 99
1012CHAIN L AND (RESSEQ 8:99 )L8 - 99
1112CHAIN Q AND (RESSEQ 8:99 )Q8 - 99
1212CHAIN R AND (RESSEQ 8:99 )R8 - 99
113CHAIN C AND (RESSEQ 30:56 OR RESSEQ 62:100 )C30 - 56
123CHAIN C AND (RESSEQ 30:56 OR RESSEQ 62:100 )C62 - 100
213CHAIN U AND (RESSEQ 30:56 OR RESSEQ 62:100 )U30 - 56
223CHAIN U AND (RESSEQ 30:56 OR RESSEQ 62:100 )U62 - 100
313CHAIN V AND (RESSEQ 30:56 OR RESSEQ 62:100 )V30 - 56
323CHAIN V AND (RESSEQ 30:56 OR RESSEQ 62:100 )V62 - 100
413CHAIN c AND (RESSEQ 30:56 OR RESSEQ 62:100 )c30 - 56
423CHAIN c AND (RESSEQ 30:56 OR RESSEQ 62:100 )c62 - 100
513CHAIN d AND (RESSEQ 30:56 OR RESSEQ 62:100 )d30 - 56
523CHAIN d AND (RESSEQ 30:56 OR RESSEQ 62:100 )d62 - 100
613CHAIN i AND (RESSEQ 30:56 OR RESSEQ 62:100 )i30 - 56
623CHAIN i AND (RESSEQ 30:56 OR RESSEQ 62:100 )i62 - 100
713CHAIN j AND (RESSEQ 30:56 OR RESSEQ 62:100 )j30 - 56
723CHAIN j AND (RESSEQ 30:56 OR RESSEQ 62:100 )j62 - 100
813CHAIN P AND (RESSEQ 30:56 OR RESSEQ 62:100 )P30 - 56
823CHAIN P AND (RESSEQ 30:56 OR RESSEQ 62:100 )P62 - 100
913CHAIN D AND (RESSEQ 30:56 OR RESSEQ 62:100 )D30 - 56
923CHAIN D AND (RESSEQ 30:56 OR RESSEQ 62:100 )D62 - 100
1013CHAIN I AND (RESSEQ 30:56 OR RESSEQ 62:100 )I30 - 56
1023CHAIN I AND (RESSEQ 30:56 OR RESSEQ 62:100 )I62 - 100
1113CHAIN J AND (RESSEQ 30:56 OR RESSEQ 62:100 )J30 - 56
1123CHAIN J AND (RESSEQ 30:56 OR RESSEQ 62:100 )J62 - 100
1213CHAIN O AND (RESSEQ 30:56 OR RESSEQ 62:100 )O30 - 56
1223CHAIN O AND (RESSEQ 30:56 OR RESSEQ 62:100 )O62 - 100

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.282101, 0.063828, -0.957259), (0.081211, -0.995792, -0.042465), (-0.955941, -0.06576, -0.286097)64.132202, -45.986401, 82.197403
2given(-0.182977, 0.196952, -0.963187), (0.806922, 0.589752, -0.0327), (0.561601, -0.7832, -0.266836)67.609497, -99.916199, -37.686901
3given(-0.531447, 0.846433, -0.033397), (-0.846707, -0.531981, -0.009159), (-0.025519, 0.023409, 0.9994)111.679001, 61.540798, 33.497898
4given(-0.473919, 0.880124, -0.027977), (-0.87266, -0.473674, -0.118732), (-0.11775, -0.031855, 0.992532)108.794998, 68.126404, -55.629902
5given(-0.070637, 0.239238, -0.968388), (0.831485, 0.550416, 0.075328), (0.551038, -0.799879, -0.237803)152.283997, -102.438004, -11.7746
6given(-0.518628, -0.854305, -0.034469), (0.85356, -0.519672, 0.037097), (-0.049605, -0.010182, 0.998717)111.873001, -63.222698, -28.1033
7given(-0.032706, -0.259761, -0.965119), (-0.886549, 0.453397, -0.091988), (0.461477, 0.852616, -0.24512)117.972, 27.393299, -13.1889
8given(0.169977, -0.160202, 0.972339), (0.906411, 0.412594, -0.090474), (-0.386687, 0.896717, 0.21534)30.5408, -41.1408, 72.043503
9given(0.489412, -0.870145, 0.057652), (-0.867401, -0.478917, 0.13511), (-0.089955, -0.116131, -0.989152)0.77945, -5.99188, 35.135601
10given(0.049036, 0.270384, 0.961503), (-0.795192, 0.593074, -0.126224), (-0.604372, -0.75839, 0.244089)101.153, 27.396299, -13.4959
11given(0.524125, 0.85067, 0.04067), (0.836393, -0.523149, 0.163587), (0.160435, -0.051723, -0.98569)108.044998, -64.431198, -10.4809
12given(-0.076017, -0.261471, -0.962213), (-0.867695, 0.492781, -0.065358), (0.49125, 0.829939, -0.264337)118.972, 25.908701, -13.454
13given(0.222032, -0.156518, 0.962395), (0.883221, 0.45043, -0.130511), (-0.413064, 0.878985, 0.23825)26.872299, -35.633801, 72.0905
14given(0.484815, -0.872721, 0.057553), (-0.868925, -0.473121, 0.145345), (-0.099616, -0.120475, -0.987706)0.776625, -5.88748, 35.049198
15given(0.014145, 0.318598, 0.947784), (-0.811617, 0.557293, -0.175221), (-0.584018, -0.76676, 0.266462)102.684998, 26.528299, -13.9054
16given(0.5278, 0.847433, 0.057307), (0.829932, -0.528898, 0.177427), (0.180667, -0.046085, -0.982464)107.813004, -64.4459, -11.348
17given(-0.520215, -0.85396, -0.011317), (0.853411, -0.520296, 0.031352), (-0.032661, 0.006651, 0.999444)111.241997, -63.0261, -28.907101
18given(0.276987, 0.015839, -0.960743), (0.049891, -0.998752, -0.002082), (-0.959578, -0.047356, -0.277432)62.5481, -43.049198, 83.339996
19given(-0.124477, 0.241048, -0.962497), (0.824748, 0.564435, 0.034695), (0.55163, -0.789499, -0.269063)60.115299, -98.296402, -36.5644
20given(-0.533065, 0.844056, -0.058404), (-0.843237, -0.535659, -0.044962), (-0.069235, 0.025281, 0.99728)111.170998, 60.039398, 35.883099
21given(-0.471401, 0.881862, -0.010019), (-0.878311, -0.470469, -0.085025), (-0.079694, -0.031281, 0.996328)107.449997, 66.479202, -58.011799
22given(-0.050016, 0.267118, -0.962365), (0.851309, 0.515282, 0.09878), (0.522275, -0.814329, -0.253172)148.865997, -104.709, -7.48065
23given(-0.511139, -0.857758, -0.054671), (0.856785, -0.513543, 0.04682), (-0.068236, -0.022909, 0.997406)112.037003, -63.733501, -27.229099
24given(-0.051485, -0.268441, -0.961919), (-0.877591, 0.471866, -0.084711), (0.476637, 0.83981, -0.259875)118.695999, 26.705601, -13.4081
25given(0.493733, -0.869373, 0.020456), (-0.866866, -0.49017, 0.090974), (-0.069064, -0.062649, -0.995643)1.76353, -5.82206, 38.638901
26given(0.205103, -0.16771, 0.964264), (0.884691, 0.453169, -0.10936), (-0.418634, 0.875506, 0.241318)27.866301, -36.532299, 72.047302
27given(0.509165, 0.86056, 0.013697), (0.852252, -0.506342, 0.131471), (0.120074, -0.055268, -0.991225)108.859001, -65.020699, -8.74783
28given(0.059571, 0.319714, 0.94564), (-0.81683, 0.560147, -0.137925), (-0.573794, -0.764211, 0.294521)102.535004, 26.6448, -14.0081
29given(-0.054579, 0.270573, -0.961151), (0.851899, 0.514734, 0.096527), (0.520855, -0.813535, -0.258594)149.345001, -104.670998, -7.1911
30given(0.315427, 0.058642, -0.947136), (0.054205, -0.997573, -0.043713), (-0.947401, -0.037551, -0.31784)61.0574, -43.7589, 82.258202
31given(-0.531096, 0.846171, -0.043945), (-0.847006, -0.531583, 0.000717), (-0.022754, 0.037603, 0.999034)111.285004, 61.823399, 33.067001
32given(-0.19782, 0.235322, -0.951573), (0.827954, 0.559783, -0.033688), (0.524746, -0.794523, -0.305572)68.309998, -101.234001, -35.1936
33given(-0.464639, 0.885475, 0.006662), (-0.883345, -0.46297, -0.073219), (-0.061749, -0.039905, 0.997294)105.528, 64.954498, -59.2173

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Components

#1: Protein
Growth/differentiation factor 2 / GDF-2 / Bone morphogenetic protein 9 / BMP-9


Mass: 12102.971 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP9, GDF2 / Plasmid: pAID4 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q9UK05
#2: Protein
Serine/threonine-protein kinase receptor R3 / SKR3 / Activin receptor-like kinase 1 / ALK-1 / TGF-B superfamily receptor type I / TSR-I


Mass: 11592.863 Da / Num. of mol.: 12 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVRL1, ACVRLK1, ALK1 / Plasmid: pAID4 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P37023
#3: Protein
Activin receptor type-2B / Activin receptor type IIB / ACTR-IIB


Mass: 14118.272 Da / Num. of mol.: 12 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ActRIIB, ACVR2B / Plasmid: pAID4 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q13705
#4: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 5, 2010 / Details: mirrors
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 82408 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 64.18 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 20.91
Reflection shellResolution: 3.35→3.41 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 4.7 / Num. unique all: 4084 / Rsym value: 0.372 / % possible all: 99.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.26 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.36 Å26.85 Å
Translation3.36 Å26.85 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: structures solved in-house, not deposited

Resolution: 3.357→26.849 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8066 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / Phase error: 26.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 1685 2.42 %random
Rwork0.219 ---
all0.22 79681 --
obs0.22 69521 84.03 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.918 Å2 / ksol: 0.289 e/Å3
Displacement parametersBiso max: 251.72 Å2 / Biso mean: 80.4386 Å2 / Biso min: 7.12 Å2
Baniso -1Baniso -2Baniso -3
1--21.5924 Å20 Å20 Å2
2---21.5924 Å20 Å2
3---17.9779 Å2
Refinement stepCycle: LAST / Resolution: 3.357→26.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25069 0 342 0 25411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01426917
X-RAY DIFFRACTIONf_angle_d1.24135486
X-RAY DIFFRACTIONf_chiral_restr0.0793834
X-RAY DIFFRACTIONf_plane_restr0.0044590
X-RAY DIFFRACTIONf_dihedral_angle_d16.1079304
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A799X-RAY DIFFRACTIONPOSITIONAL0.064
12B799X-RAY DIFFRACTIONPOSITIONAL0.064
13G795X-RAY DIFFRACTIONPOSITIONAL0.065
14H806X-RAY DIFFRACTIONPOSITIONAL0.048
15M802X-RAY DIFFRACTIONPOSITIONAL0.054
16N796X-RAY DIFFRACTIONPOSITIONAL0.067
17S806X-RAY DIFFRACTIONPOSITIONAL0.044
18T798X-RAY DIFFRACTIONPOSITIONAL0.067
19a796X-RAY DIFFRACTIONPOSITIONAL0.066
110b806X-RAY DIFFRACTIONPOSITIONAL0.051
111g806X-RAY DIFFRACTIONPOSITIONAL0.064
112h806X-RAY DIFFRACTIONPOSITIONAL0.051
21E707X-RAY DIFFRACTIONPOSITIONAL0.049
22X707X-RAY DIFFRACTIONPOSITIONAL0.049
23e713X-RAY DIFFRACTIONPOSITIONAL0.052
24f717X-RAY DIFFRACTIONPOSITIONAL0.056
25k703X-RAY DIFFRACTIONPOSITIONAL0.056
26l709X-RAY DIFFRACTIONPOSITIONAL0.053
27W720X-RAY DIFFRACTIONPOSITIONAL0.037
28F711X-RAY DIFFRACTIONPOSITIONAL0.057
29K706X-RAY DIFFRACTIONPOSITIONAL0.06
210L719X-RAY DIFFRACTIONPOSITIONAL0.056
211Q729X-RAY DIFFRACTIONPOSITIONAL0.04
212R713X-RAY DIFFRACTIONPOSITIONAL0.061
31C495X-RAY DIFFRACTIONPOSITIONAL0.034
32U495X-RAY DIFFRACTIONPOSITIONAL0.034
33V491X-RAY DIFFRACTIONPOSITIONAL0.04
34c492X-RAY DIFFRACTIONPOSITIONAL0.039
35d487X-RAY DIFFRACTIONPOSITIONAL0.041
36i496X-RAY DIFFRACTIONPOSITIONAL0.039
37j497X-RAY DIFFRACTIONPOSITIONAL0.042
38P491X-RAY DIFFRACTIONPOSITIONAL0.043
39D497X-RAY DIFFRACTIONPOSITIONAL0.042
310I488X-RAY DIFFRACTIONPOSITIONAL0.034
311J481X-RAY DIFFRACTIONPOSITIONAL0.045
312O470X-RAY DIFFRACTIONPOSITIONAL0.04
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.357-3.47640.34361600.28636454661480
3.4764-3.61530.30191600.25686557671781
3.6153-3.77940.26321650.23466806697185
3.7794-3.97810.27311680.20756354652279
3.9781-4.22640.22911630.20326194635777
4.2264-4.55130.23311670.19176788695584
4.5513-5.00660.25241610.19436776693784
5.0066-5.7250.29851750.23237002717787
5.725-7.18980.24571760.22527215739189
7.1898-26.84950.23981900.21187690788093
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.63440.6821-0.20611.2983-0.40250.0636-0.1729-0.0449-0.0036-0.30110.10380.13080.0548-0.10910.06240.11460.0327-0.02860.03360.01190.10786.573-10.5574-1.4267
20.92680.5044-0.11950.6094-0.52360.9982-0.23060.087-0.42550.12620.0131-0.3020.14-0.0880.22870.171-0.0760.09860.06870.02970.251389.2508-28.39281.0495
31.2190.30220.9960.8850.14130.9017-0.0241-0.5360.23040.5975-0.2996-0.2939-0.2045-0.14510.13230.3699-0.0293-0.2120.39640.08570.175897.2401-6.334519.9899
40.12780.0476-0.09710.05790.00850.1535-0.07090.1236-0.1016-0.1612-0.0574-0.06240.1748-0.13430.06760.3088-0.17380.10710.4126-0.12780.249472.5143-32.4906-16.3616
51.5728-0.1044-0.5290.35960.23540.4305-0.31250.36220.15950.1380.1072-0.05820.0509-0.18470.07970.3016-0.0094-0.01490.23190.11980.139195.886313.2469-9.587
61.9041-0.23871.2510.1464-0.56472.63350.4636-0.1871-0.8389-0.37890.3903-0.33240.94440.23210.1898-0.51260.38370.71230.1377-0.13310.8015100.828-51.5278-6.3886
70.668-0.52750.88091.9991-0.70741.119-0.06540.11230.23190.0548-0.2541-0.7068-0.10570.240.39070.0543-0.0281-0.0650.15520.09140.290789.019528.1053-30.7584
82.5761-0.67090.19050.40730.0890.1903-0.00720.4229-0.2370.0473-0.04550.05990.11460.06040.05140.14550.0024-0.04930.08550.03710.175875.279816.2975-33.4083
94.05870.0690.42290.71370.07170.2399-0.1106-1.39380.12130.2492-0.10810.1438-0.2611-0.21660.08510.2079-0.03890.05640.4876-0.16420.098665.498923.7254-12.6227
100.72370.1061-0.2180.9514-0.23751.4674-0.22750.61810.2121-0.492-0.2536-0.08740.34690.16910.32860.31480.18740.05420.58610.15950.1941101.304616.0772-48.1992
110.56880.06380.10390.14830.31391.29710.09330.12360.7380.11390.3709-0.2516-0.86040.3087-0.2550.6511-0.0883-0.16140.34610.42951.3493102.834350.0861-37.9929
121.3367-0.1307-0.30570.8236-1.33372.51260.02320.3349-0.4621-0.2102-0.3548-0.05070.6930.2653-0.07140.2543-0.0255-0.11010.189-0.05230.006550.608110.9915-42.1804
131.36140.19360.08410.5951-0.02080.0835-0.16940.071-0.43320.35850.012-0.3360.01170.1870.08430.12070.0596-0.0650.26620.00940.219372.691415.969463.6747
140.543-0.51260.95311.9966-1.24632.0714-0.2356-0.03470.22980.4357-0.3107-1.0019-0.24340.01990.45740.20540.0359-0.31670.26030.00360.569186.761826.563267.9193
152.48340.41720.2911.9275-1.42181.18670.0368-1.312-0.10391.1815-0.0768-0.0219-0.7789-0.01710.05560.86530.20710.02341.041-0.22240.468561.772622.483184.2479
160.7704-0.61120.15741.6474-1.02861.9835-0.16670.53330.4413-0.3688-0.533-0.6670.24450.18110.45560.10240.16830.04490.61670.21410.4671100.430114.484352.0847
170.05370.0669-0.05630.99480.01290.20520.0702-0.08450.00460.4262-0.2169-0.11890.04140.25110.01650.20540.0323-0.10910.3236-0.03810.099848.141113.037953.122
180.22470.19130.16090.34110.05321.12760.0765-0.20920.04220.70470.1202-0.7921-1.00510.22810.03090.9591-0.1336-0.62690.45690.42421.5529102.2448.21963.1248
190.0496-0.384-0.00472.01980.1460.07330.11550.1133-0.0062-0.155-0.2242-0.2406-0.0215-0.03790.07550.06450.0225-0.01330.0908-0.01180.074756.7666-6.030829.4579
200.42980.098-0.02090.53390.41060.5456-0.2773-0.21450.13620.0360.0270.3109-0.0084-0.06280.06670.11010.0703-0.06810.0995-0.07050.199640.15010.961430.9807
210.8792-0.2936-0.11741.1561-0.90751.2901-0.2952-0.3086-0.36290.6667-0.01010.12120.0224-0.10040.09550.37680.03150.17650.28040.11440.320953.722-17.765150.614
220.56070.0589-0.08770.6511-0.32590.68880.06790.32250.075-0.3744-0.32910.0423-0.13520.38460.18550.49990.0417-0.06690.2690.01610.091346.347117.813514.2813
231.08060.18110.35510.6173-0.38940.4931-0.2643-0.2615-0.14210.09790.004-0.0335-0.33480.02940.19410.30340.0460.00520.259-0.04830.08172.6807-26.526822.0839
240.57410.7748-0.53141.49290.07871.8390.2784-0.04110.563-0.0661-0.03821.03410.1264-0.9332-0.03190.3194-0.0918-0.27340.5142-0.22871.160914.58343.513622.0327
250.4215-0.21160.24050.8119-0.76110.7093-0.25780.23620.2864-0.0858-0.0838-0.3316-0.25370.14960.27120.4596-0.05280.06780.18320.16620.368565.832-62.163936.0266
260.2920.2355-0.16741.2484-0.35530.10940.16980.00560.3784-0.0873-0.23120.5994-0.2647-0.0046-0.0110.275-0.00770.05230.10620.0840.464749.2271-68.232540.5066
271.9228-0.39020.02342.87040.22120.0386-0.13940.7933-0.1192-1.67840.10040.12140.25540.02390.08350.83230.03190.09960.37270.05940.280348.8431-81.998820.4947
280.53770.13230.10190.65640.0350.1383-0.0914-0.27870.1110.6111-0.1855-0.0707-0.3419-0.03890.20720.72360.0044-0.03670.2670.11640.370362.5289-43.741851.2893
290.8653-0.9918-0.72651.37080.24831.93850.52020.04820.3663-0.2333-0.1479-0.97660.06510.78060.060.45130.1582-0.06530.63610.56451.239292.1079-60.37240.5932
301.75270.57521.27161.51370.4632.9854-0.10030.20760.56460.3951-0.11890.7603-0.5884-0.1545-0.18350.31710.04170.20550.24140.07570.431833.8255-86.781852.1163
310.80820.45480.58060.30130.42391.1267-0.14470.40160.30420.0057-0.04150.13480.0838-0.0708-0.15110.1563-0.0754-0.21540.2430.03160.287622.1834-35.5949-6.2959
322.48751.0640.22030.42620.03020.2202-0.03610.0445-0.5607-0.11440.079-0.14230.167-0.0204-0.29240.1218-0.0267-0.10410.07450.02030.201135.2617-46.9272-0.9818
332.15460.11920.14280.41390.37190.3816-0.5931.1734-0.2148-0.30520.19130.1034-0.05060.04260.28820.4956-0.1373-0.0780.79810.01280.268247.7631-41.0736-20.8787
341.54910.16020.29780.6597-0.32130.8433-0.2112-0.4767-0.26850.3019-0.2244-0.15440.05-0.20460.21270.3296-0.1901-0.06480.33010.02770.18887.4878-46.18789.9582
350.31690.25590.07950.7322-0.5630.9169-0.03530.00640.0784-0.30650.34310.5942-0.7061-0.1167-0.11820.7952-0.1302-0.40120.2684-0.09291.0937.6177-13.0152-2.797
362.53230.8029-0.79260.8111-0.23461.42340.1535-0.288-0.69150.0055-0.4297-0.07670.3995-0.18550.07160.2975-0.0352-0.14160.29090.07190.214558.8553-51.383311.0555
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 6:110)A6 - 110
2X-RAY DIFFRACTION2(CHAIN B AND RESID 6:110)B6 - 110
3X-RAY DIFFRACTION3(CHAIN C AND RESID 30:104)C30 - 104
4X-RAY DIFFRACTION4(CHAIN D AND RESID 30:101)D30 - 101
5X-RAY DIFFRACTION5(CHAIN E AND RESID 9:99)E9 - 99
6X-RAY DIFFRACTION6(CHAIN F AND RESID 9:99)F9 - 99
7X-RAY DIFFRACTION7(CHAIN G AND RESID 6:110)G6 - 110
8X-RAY DIFFRACTION8(CHAIN H AND RESID 6:110)H6 - 110
9X-RAY DIFFRACTION9(CHAIN I AND RESID 30:104)I30 - 104
10X-RAY DIFFRACTION10(CHAIN J AND RESID 30:101)J30 - 101
11X-RAY DIFFRACTION11(CHAIN K AND RESID 9:99)K9 - 99
12X-RAY DIFFRACTION12(CHAIN L AND RESID 9:99)L9 - 99
13X-RAY DIFFRACTION13(CHAIN M AND RESID 6:110)M6 - 110
14X-RAY DIFFRACTION14(CHAIN N AND RESID 7:110)N7 - 110
15X-RAY DIFFRACTION15(CHAIN O AND RESID 30:104)O30 - 104
16X-RAY DIFFRACTION16(CHAIN P AND RESID 30:101)P30 - 101
17X-RAY DIFFRACTION17(CHAIN Q AND RESID 9:99)Q9 - 99
18X-RAY DIFFRACTION18(CHAIN R AND RESID 9:99)R9 - 99
19X-RAY DIFFRACTION19(CHAIN S AND RESID 6:110)S6 - 110
20X-RAY DIFFRACTION20(CHAIN T AND RESID 6:110)T6 - 110
21X-RAY DIFFRACTION21(CHAIN U AND RESID 30:104)U30 - 104
22X-RAY DIFFRACTION22(CHAIN V AND RESID 30:101)V30 - 101
23X-RAY DIFFRACTION23(CHAIN W AND RESID 9:99)W9 - 99
24X-RAY DIFFRACTION24(CHAIN X AND RESID 9:99)X9 - 99
25X-RAY DIFFRACTION25(CHAIN a AND RESID 6:110)a6 - 110
26X-RAY DIFFRACTION26(CHAIN b AND RESID 6:110)b6 - 110
27X-RAY DIFFRACTION27(CHAIN c AND RESID 30:104)c30 - 104
28X-RAY DIFFRACTION28(CHAIN d AND RESID 30:101)d30 - 101
29X-RAY DIFFRACTION29(CHAIN e AND RESID 9:99)e9 - 99
30X-RAY DIFFRACTION30(CHAIN f AND RESID 9:99)f9 - 99
31X-RAY DIFFRACTION31(CHAIN g AND RESID 6:110)g6 - 110
32X-RAY DIFFRACTION32(CHAIN h AND RESID 6:110)h6 - 110
33X-RAY DIFFRACTION33(CHAIN i AND RESID 30:104)i30 - 104
34X-RAY DIFFRACTION34(CHAIN j AND RESID 30:101)j30 - 101
35X-RAY DIFFRACTION35(CHAIN k AND RESID 9:99)k9 - 99
36X-RAY DIFFRACTION36(CHAIN l AND RESID 9:99)l9 - 99

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