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- PDB-6nmr: Blocking Fab 119 anti-SIRP-alpha antibody in complex with SIRP-al... -

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Basic information

Entry
Database: PDB / ID: 6nmr
TitleBlocking Fab 119 anti-SIRP-alpha antibody in complex with SIRP-alpha Variant 1
Components
  • Fab 119 anti-SIRP-alpha antibody Variable Heavy Chain
  • Fab 119 anti-SIRP-alpha antibody Variable Light Chain
  • Tyrosine-protein phosphatase non-receptor type substrate 1
KeywordsIMMUNE SYSTEM / SIRP-alpha / Signal regulatory protein alpha / Signal-regulatory protein alpha / Tyrosine-protein phosphatase non-receptor type substrate 1 / CD47 / Cluster of Differentiation 47 / anti-SIRP-alpha antibody / Blocking anti-SIRP-alpha antibody / Non-Blocking anti-SIRP-alpha antibody / Kick-Off anti-SIRP-alpha antibody / anti-SIRP-alpha antibody in complex with SIRP-alpha
Function / homology
Function and homology information


negative regulation of I-kappaB phosphorylation / cellular response to interleukin-12 / monocyte extravasation / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / protein binding involved in heterotypic cell-cell adhesion / regulation of interleukin-1 beta production / regulation of type II interferon production / cell-cell adhesion mediator activity / GTPase regulator activity ...negative regulation of I-kappaB phosphorylation / cellular response to interleukin-12 / monocyte extravasation / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / protein binding involved in heterotypic cell-cell adhesion / regulation of interleukin-1 beta production / regulation of type II interferon production / cell-cell adhesion mediator activity / GTPase regulator activity / protein antigen binding / negative regulation of nitric oxide biosynthetic process / negative regulation of interferon-beta production / negative regulation of JNK cascade / regulation of tumor necrosis factor production / regulation of nitric oxide biosynthetic process / negative regulation of phagocytosis / regulation of interleukin-6 production / Signal regulatory protein family interactions / tertiary granule membrane / negative regulation of interleukin-6 production / ficolin-1-rich granule membrane / negative regulation of tumor necrosis factor production / negative regulation of cytokine production involved in inflammatory response / cellular response to interleukin-1 / positive regulation of phagocytosis / protein tyrosine kinase binding / negative regulation of protein phosphorylation / Cell surface interactions at the vascular wall / negative regulation of ERK1 and ERK2 cascade / cellular response to hydrogen peroxide / negative regulation of inflammatory response / SH3 domain binding / cellular response to type II interferon / positive regulation of T cell activation / cell migration / regulation of gene expression / protein phosphatase binding / cellular response to lipopolysaccharide / cell adhesion / Neutrophil degranulation / cell surface / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.42 Å
AuthorsWibowo, A.S. / Carter, J.J. / Sim, J.
CitationJournal: Mabs / Year: 2019
Title: Discovery of high affinity, pan-allelic, and pan-mammalian reactive antibodies against the myeloid checkpoint receptor SIRP alpha.
Authors: Sim, J. / Sockolosky, J.T. / Sangalang, E. / Izquierdo, S. / Pedersen, D. / Harriman, W. / Wibowo, A.S. / Carter, J. / Madan, A. / Doyle, L. / Harrabi, O. / Kauder, S.E. / Chen, A. / Kuo, T. ...Authors: Sim, J. / Sockolosky, J.T. / Sangalang, E. / Izquierdo, S. / Pedersen, D. / Harriman, W. / Wibowo, A.S. / Carter, J. / Madan, A. / Doyle, L. / Harrabi, O. / Kauder, S.E. / Chen, A. / Kuo, T.C. / Wan, H. / Pons, J.
History
DepositionJan 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab 119 anti-SIRP-alpha antibody Variable Light Chain
H: Fab 119 anti-SIRP-alpha antibody Variable Heavy Chain
S: Tyrosine-protein phosphatase non-receptor type substrate 1
B: Fab 119 anti-SIRP-alpha antibody Variable Light Chain
A: Fab 119 anti-SIRP-alpha antibody Variable Heavy Chain
E: Tyrosine-protein phosphatase non-receptor type substrate 1
G: Fab 119 anti-SIRP-alpha antibody Variable Light Chain
F: Fab 119 anti-SIRP-alpha antibody Variable Heavy Chain
I: Tyrosine-protein phosphatase non-receptor type substrate 1
K: Fab 119 anti-SIRP-alpha antibody Variable Light Chain
J: Fab 119 anti-SIRP-alpha antibody Variable Heavy Chain
M: Tyrosine-protein phosphatase non-receptor type substrate 1


Theoretical massNumber of molelcules
Total (without water)248,94912
Polymers248,94912
Non-polymers00
Water6,161342
1
L: Fab 119 anti-SIRP-alpha antibody Variable Light Chain
H: Fab 119 anti-SIRP-alpha antibody Variable Heavy Chain
S: Tyrosine-protein phosphatase non-receptor type substrate 1


Theoretical massNumber of molelcules
Total (without water)62,2373
Polymers62,2373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-34 kcal/mol
Surface area23920 Å2
MethodPISA
2
B: Fab 119 anti-SIRP-alpha antibody Variable Light Chain
A: Fab 119 anti-SIRP-alpha antibody Variable Heavy Chain
E: Tyrosine-protein phosphatase non-receptor type substrate 1


Theoretical massNumber of molelcules
Total (without water)62,2373
Polymers62,2373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-35 kcal/mol
Surface area24160 Å2
MethodPISA
3
G: Fab 119 anti-SIRP-alpha antibody Variable Light Chain
F: Fab 119 anti-SIRP-alpha antibody Variable Heavy Chain
I: Tyrosine-protein phosphatase non-receptor type substrate 1


Theoretical massNumber of molelcules
Total (without water)62,2373
Polymers62,2373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-32 kcal/mol
Surface area24200 Å2
MethodPISA
4
K: Fab 119 anti-SIRP-alpha antibody Variable Light Chain
J: Fab 119 anti-SIRP-alpha antibody Variable Heavy Chain
M: Tyrosine-protein phosphatase non-receptor type substrate 1


Theoretical massNumber of molelcules
Total (without water)62,2373
Polymers62,2373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-33 kcal/mol
Surface area24160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.070, 113.560, 152.080
Angle α, β, γ (deg.)90.000, 91.350, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN B AND (RESID 2 THROUGH 6 OR RESID 8...
21(CHAIN E AND (RESID 2 THROUGH 6 OR RESID 8...
31(CHAIN H AND (RESID 2 THROUGH 6 OR RESID 8...
41(CHAIN K AND (RESID 2 THROUGH 6 OR RESID 8...
12(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...
22(CHAIN D AND (RESID 1 THROUGH 16 OR RESID 19...
32(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...
42(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...
13(CHAIN J AND (RESID 4 THROUGH 10 OR RESID 13...
23(CHAIN F AND (RESID 4 THROUGH 10 OR RESID 13...
33(CHAIN I AND (RESID 4 THROUGH 10 OR RESID 13...
43(CHAIN L AND (RESID 4 THROUGH 10 OR RESID 13...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(CHAIN B AND (RESID 2 THROUGH 6 OR RESID 8...B2
121(CHAIN B AND (RESID 2 THROUGH 6 OR RESID 8...B8
131(CHAIN B AND (RESID 2 THROUGH 6 OR RESID 8...B14
141(CHAIN B AND (RESID 2 THROUGH 6 OR RESID 8...B32
151(CHAIN B AND (RESID 2 THROUGH 6 OR RESID 8...B51
161(CHAIN B AND (RESID 2 THROUGH 6 OR RESID 8...B54
171(CHAIN B AND (RESID 2 THROUGH 6 OR RESID 8...B62
181(CHAIN B AND (RESID 2 THROUGH 6 OR RESID 8...B72
191(CHAIN B AND (RESID 2 THROUGH 6 OR RESID 8...B75
1101(CHAIN B AND (RESID 2 THROUGH 6 OR RESID 8...B86
1111(CHAIN B AND (RESID 2 THROUGH 6 OR RESID 8...B88
1121(CHAIN B AND (RESID 2 THROUGH 6 OR RESID 8...B94
1131(CHAIN B AND (RESID 2 THROUGH 6 OR RESID 8...B99
1141(CHAIN B AND (RESID 2 THROUGH 6 OR RESID 8...B141
1151(CHAIN B AND (RESID 2 THROUGH 6 OR RESID 8...B168
1161(CHAIN B AND (RESID 2 THROUGH 6 OR RESID 8...B209
1171(CHAIN B AND (RESID 2 THROUGH 6 OR RESID 8...B214
211(CHAIN E AND (RESID 2 THROUGH 6 OR RESID 8...E2
221(CHAIN E AND (RESID 2 THROUGH 6 OR RESID 8...E8
231(CHAIN E AND (RESID 2 THROUGH 6 OR RESID 8...E14
241(CHAIN E AND (RESID 2 THROUGH 6 OR RESID 8...E32
251(CHAIN E AND (RESID 2 THROUGH 6 OR RESID 8...E51
261(CHAIN E AND (RESID 2 THROUGH 6 OR RESID 8...E54
271(CHAIN E AND (RESID 2 THROUGH 6 OR RESID 8...E62
281(CHAIN E AND (RESID 2 THROUGH 6 OR RESID 8...E72
291(CHAIN E AND (RESID 2 THROUGH 6 OR RESID 8...E75
2101(CHAIN E AND (RESID 2 THROUGH 6 OR RESID 8...E86
2111(CHAIN E AND (RESID 2 THROUGH 6 OR RESID 8...E88
2121(CHAIN E AND (RESID 2 THROUGH 6 OR RESID 8...E94
2131(CHAIN E AND (RESID 2 THROUGH 6 OR RESID 8...E99
2141(CHAIN E AND (RESID 2 THROUGH 6 OR RESID 8...E141
2151(CHAIN E AND (RESID 2 THROUGH 6 OR RESID 8...E168
2161(CHAIN E AND (RESID 2 THROUGH 6 OR RESID 8...E209
2171(CHAIN E AND (RESID 2 THROUGH 6 OR RESID 8...E214
311(CHAIN H AND (RESID 2 THROUGH 6 OR RESID 8...H2
321(CHAIN H AND (RESID 2 THROUGH 6 OR RESID 8...H8
331(CHAIN H AND (RESID 2 THROUGH 6 OR RESID 8...H14
341(CHAIN H AND (RESID 2 THROUGH 6 OR RESID 8...H32
351(CHAIN H AND (RESID 2 THROUGH 6 OR RESID 8...H51
361(CHAIN H AND (RESID 2 THROUGH 6 OR RESID 8...H54
371(CHAIN H AND (RESID 2 THROUGH 6 OR RESID 8...H62
381(CHAIN H AND (RESID 2 THROUGH 6 OR RESID 8...H72
391(CHAIN H AND (RESID 2 THROUGH 6 OR RESID 8...H75
3101(CHAIN H AND (RESID 2 THROUGH 6 OR RESID 8...H86
3111(CHAIN H AND (RESID 2 THROUGH 6 OR RESID 8...H88
3121(CHAIN H AND (RESID 2 THROUGH 6 OR RESID 8...H94
3131(CHAIN H AND (RESID 2 THROUGH 6 OR RESID 8...H99
3141(CHAIN H AND (RESID 2 THROUGH 6 OR RESID 8...H141
3151(CHAIN H AND (RESID 2 THROUGH 6 OR RESID 8...H168
3161(CHAIN H AND (RESID 2 THROUGH 6 OR RESID 8...H209
3171(CHAIN H AND (RESID 2 THROUGH 6 OR RESID 8...H214
411(CHAIN K AND (RESID 2 THROUGH 6 OR RESID 8...K2
421(CHAIN K AND (RESID 2 THROUGH 6 OR RESID 8...K8
431(CHAIN K AND (RESID 2 THROUGH 6 OR RESID 8...K14
441(CHAIN K AND (RESID 2 THROUGH 6 OR RESID 8...K32
451(CHAIN K AND (RESID 2 THROUGH 6 OR RESID 8...K51
461(CHAIN K AND (RESID 2 THROUGH 6 OR RESID 8...K54
471(CHAIN K AND (RESID 2 THROUGH 6 OR RESID 8...K62
481(CHAIN K AND (RESID 2 THROUGH 6 OR RESID 8...K72
491(CHAIN K AND (RESID 2 THROUGH 6 OR RESID 8...K75
4101(CHAIN K AND (RESID 2 THROUGH 6 OR RESID 8...K86
4111(CHAIN K AND (RESID 2 THROUGH 6 OR RESID 8...K88
4121(CHAIN K AND (RESID 2 THROUGH 6 OR RESID 8...K94
4131(CHAIN K AND (RESID 2 THROUGH 6 OR RESID 8...K99
4141(CHAIN K AND (RESID 2 THROUGH 6 OR RESID 8...K141
4151(CHAIN K AND (RESID 2 THROUGH 6 OR RESID 8...K168
4161(CHAIN K AND (RESID 2 THROUGH 6 OR RESID 8...K209
4171(CHAIN K AND (RESID 2 THROUGH 6 OR RESID 8...K214
112(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A1
122(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A19
132(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A25
142(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A32
152(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A43
162(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A46
172(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A53
182(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A55
192(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A61
1102(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A68
1112(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A95
1122(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A99
1132(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A107
1142(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A128
1152(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A147
1162(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A149
1172(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A162
1182(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A167
1192(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A171
1202(CHAIN A AND (RESID 1 THROUGH 16 OR RESID 19...A190
212(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H1
222(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H19
232(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H25
242(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H32
252(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H43
262(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H46
272(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H53
282(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H55
292(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H61
2102(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H68
2112(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H95
2122(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H99
2132(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H107
2142(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H128
2152(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H147
2162(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H149
2172(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H162
2182(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H167
2192(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H171
2202(CHAIN H AND (RESID 1 THROUGH 16 OR RESID 19...H190
312(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G1
322(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G19
332(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G25
342(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G32
352(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G43
362(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G46
372(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G53
382(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G55
392(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G61
3102(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G68
3112(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G95
3122(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G99
3132(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G107
3142(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G128
3152(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G147
3162(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G149
3172(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G162
3182(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G167
3192(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G171
3202(CHAIN G AND (RESID 1 THROUGH 16 OR RESID 19...G190
412(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J1
422(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J19
432(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J25
442(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J32
452(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J43
462(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J46
472(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J53
482(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J55
492(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J61
4102(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J68
4112(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J95
4122(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J99
4132(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J107
4142(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J128
4152(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J147
4162(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J149
4172(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J162
4182(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J167
4192(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J171
4202(CHAIN J AND (RESID 1 THROUGH 16 OR RESID 19...J190
113(CHAIN J AND (RESID 4 THROUGH 10 OR RESID 13...J4
123(CHAIN J AND (RESID 4 THROUGH 10 OR RESID 13...J13
133(CHAIN J AND (RESID 4 THROUGH 10 OR RESID 13...J16
143(CHAIN J AND (RESID 4 THROUGH 10 OR RESID 13...J29
153(CHAIN J AND (RESID 4 THROUGH 10 OR RESID 13...J48
163(CHAIN J AND (RESID 4 THROUGH 10 OR RESID 13...J50
173(CHAIN J AND (RESID 4 THROUGH 10 OR RESID 13...J54
183(CHAIN J AND (RESID 4 THROUGH 10 OR RESID 13...J69
193(CHAIN J AND (RESID 4 THROUGH 10 OR RESID 13...J74
1103(CHAIN J AND (RESID 4 THROUGH 10 OR RESID 13...J82
1113(CHAIN J AND (RESID 4 THROUGH 10 OR RESID 13...J91
1123(CHAIN J AND (RESID 4 THROUGH 10 OR RESID 13...J94
1133(CHAIN J AND (RESID 4 THROUGH 10 OR RESID 13...J104
1143(CHAIN J AND (RESID 4 THROUGH 10 OR RESID 13...J106
1153(CHAIN J AND (RESID 4 THROUGH 10 OR RESID 13...J112
213(CHAIN F AND (RESID 4 THROUGH 10 OR RESID 13...F4
223(CHAIN F AND (RESID 4 THROUGH 10 OR RESID 13...F13
233(CHAIN F AND (RESID 4 THROUGH 10 OR RESID 13...F16
243(CHAIN F AND (RESID 4 THROUGH 10 OR RESID 13...F29
253(CHAIN F AND (RESID 4 THROUGH 10 OR RESID 13...F48
263(CHAIN F AND (RESID 4 THROUGH 10 OR RESID 13...F50
273(CHAIN F AND (RESID 4 THROUGH 10 OR RESID 13...F54
283(CHAIN F AND (RESID 4 THROUGH 10 OR RESID 13...F69
293(CHAIN F AND (RESID 4 THROUGH 10 OR RESID 13...F74
2103(CHAIN F AND (RESID 4 THROUGH 10 OR RESID 13...F82
2113(CHAIN F AND (RESID 4 THROUGH 10 OR RESID 13...F91
2123(CHAIN F AND (RESID 4 THROUGH 10 OR RESID 13...F94
2133(CHAIN F AND (RESID 4 THROUGH 10 OR RESID 13...F104
2143(CHAIN F AND (RESID 4 THROUGH 10 OR RESID 13...F106
2153(CHAIN F AND (RESID 4 THROUGH 10 OR RESID 13...F112
313(CHAIN I AND (RESID 4 THROUGH 10 OR RESID 13...I4
323(CHAIN I AND (RESID 4 THROUGH 10 OR RESID 13...I13
333(CHAIN I AND (RESID 4 THROUGH 10 OR RESID 13...I16
343(CHAIN I AND (RESID 4 THROUGH 10 OR RESID 13...I29
353(CHAIN I AND (RESID 4 THROUGH 10 OR RESID 13...I48
363(CHAIN I AND (RESID 4 THROUGH 10 OR RESID 13...I50
373(CHAIN I AND (RESID 4 THROUGH 10 OR RESID 13...I54
383(CHAIN I AND (RESID 4 THROUGH 10 OR RESID 13...I69
393(CHAIN I AND (RESID 4 THROUGH 10 OR RESID 13...I74
3103(CHAIN I AND (RESID 4 THROUGH 10 OR RESID 13...I82
3113(CHAIN I AND (RESID 4 THROUGH 10 OR RESID 13...I91
3123(CHAIN I AND (RESID 4 THROUGH 10 OR RESID 13...I94
3133(CHAIN I AND (RESID 4 THROUGH 10 OR RESID 13...I104
3143(CHAIN I AND (RESID 4 THROUGH 10 OR RESID 13...I106
3153(CHAIN I AND (RESID 4 THROUGH 10 OR RESID 13...I112
413(CHAIN L AND (RESID 4 THROUGH 10 OR RESID 13...L4
423(CHAIN L AND (RESID 4 THROUGH 10 OR RESID 13...L13
433(CHAIN L AND (RESID 4 THROUGH 10 OR RESID 13...L16
443(CHAIN L AND (RESID 4 THROUGH 10 OR RESID 13...L29
453(CHAIN L AND (RESID 4 THROUGH 10 OR RESID 13...L48
463(CHAIN L AND (RESID 4 THROUGH 10 OR RESID 13...L50
473(CHAIN L AND (RESID 4 THROUGH 10 OR RESID 13...L54
483(CHAIN L AND (RESID 4 THROUGH 10 OR RESID 13...L69
493(CHAIN L AND (RESID 4 THROUGH 10 OR RESID 13...L74
4103(CHAIN L AND (RESID 4 THROUGH 10 OR RESID 13...L82
4113(CHAIN L AND (RESID 4 THROUGH 10 OR RESID 13...L91
4123(CHAIN L AND (RESID 4 THROUGH 10 OR RESID 13...L94
4133(CHAIN L AND (RESID 4 THROUGH 10 OR RESID 13...L104
4143(CHAIN L AND (RESID 4 THROUGH 10 OR RESID 13...L106
4153(CHAIN L AND (RESID 4 THROUGH 10 OR RESID 13...L112

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody
Fab 119 anti-SIRP-alpha antibody Variable Light Chain


Mass: 23819.436 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
Fab 119 anti-SIRP-alpha antibody Variable Heavy Chain


Mass: 24386.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein
Tyrosine-protein phosphatase non-receptor type substrate 1 / SHPS-1 / Brain Ig-like molecule with tyrosine-based activation motifs / Bit / CD172 antigen-like ...SHPS-1 / Brain Ig-like molecule with tyrosine-based activation motifs / Bit / CD172 antigen-like family member A / Inhibitory receptor SHPS-1 / Macrophage fusion receptor / MyD-1 antigen / Signal-regulatory protein alpha-1 / Sirp-alpha-1 / Signal-regulatory protein alpha-2 / Sirp-alpha-2 / Signal-regulatory protein alpha-3 / Sirp-alpha-3 / p84


Mass: 14031.807 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRPA, BIT, MFR, MYD1, PTPNS1, SHPS1, SIRP / Production host: Homo sapiens (human) / References: UniProt: P78324
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 0.2 M MgCl2, 15% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07822 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 23, 2017
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07822 Å / Relative weight: 1
ReflectionResolution: 2.42→38.01 Å / Num. obs: 79584 / % possible obs: 97.6 % / Redundancy: 3.7 % / Rsym value: 0.156 / Net I/σ(I): 7.3
Reflection shellResolution: 2.42→2.48 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5911 / Rsym value: 0.0849 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
xia2data scaling
PHASERphasing
RefinementResolution: 2.42→38.009 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.68
RfactorNum. reflection% reflection
Rfree0.3232 4000 5.03 %
Rwork0.2885 --
obs0.2902 79558 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.95 Å2 / Biso mean: 47.8759 Å2 / Biso min: 22.02 Å2
Refinement stepCycle: final / Resolution: 2.42→38.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16257 0 0 342 16599
Biso mean---42.47 -
Num. residues----2171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00516651
X-RAY DIFFRACTIONf_angle_d1.02422705
X-RAY DIFFRACTIONf_chiral_restr0.0552570
X-RAY DIFFRACTIONf_plane_restr0.0082933
X-RAY DIFFRACTIONf_dihedral_angle_d11.6679796
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B3219X-RAY DIFFRACTIONPOSITIONAL0
12E3219X-RAY DIFFRACTIONPOSITIONAL0
13H3219X-RAY DIFFRACTIONPOSITIONAL0
14K3219X-RAY DIFFRACTIONPOSITIONAL0
21A3215X-RAY DIFFRACTIONPOSITIONAL0
22H3215X-RAY DIFFRACTIONPOSITIONAL0
23G3215X-RAY DIFFRACTIONPOSITIONAL0
24J3215X-RAY DIFFRACTIONPOSITIONAL0
31J1378X-RAY DIFFRACTIONPOSITIONAL0
32F1378X-RAY DIFFRACTIONPOSITIONAL0
33I1378X-RAY DIFFRACTIONPOSITIONAL0
34L1378X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.42-2.44850.37411190.35392610272999
2.4485-2.47830.3721540.34092597275198
2.4783-2.50970.3931400.34972633277398
2.5097-2.54270.35561490.34772607275698
2.5427-2.57750.41511530.3472576272998
2.5775-2.61440.39291550.3572627278298
2.6144-2.65340.3911620.36232600276298
2.6534-2.69480.42291340.37052584271898
2.6948-2.7390.39961590.36152625278498
2.739-2.78620.38941460.36952580272698
2.7862-2.83690.38791350.35272648278398
2.8369-2.89140.39321230.35852588271198
2.8914-2.95040.44241180.35522553267195
2.9504-3.01450.35761420.35672412255489
3.0145-3.08460.41021120.34492537264996
3.0846-3.16170.36371400.33242680282098
3.1617-3.24720.38161260.32152633275999
3.2472-3.34270.38811490.30592612276198
3.3427-3.45050.29531320.28512621275398
3.4505-3.57370.28721480.27432609275798
3.5737-3.71670.31961410.27872680282198
3.7167-3.88570.31791220.27452621274398
3.8857-4.09030.32761270.26712613274098
4.0903-4.34630.30521410.25082637277898
4.3463-4.68130.25081240.23882629275398
4.6813-5.15130.25911620.23882613277597
5.1513-5.89440.26881220.25492458258091
5.8944-7.41720.29681410.27322659280098
7.4172-38.01410.24171240.22692716284098

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