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- PDB-3nh7: Crystal structure of the neutralizing Fab fragment AbD1556 bound ... -

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Basic information

Entry
Database: PDB / ID: 3nh7
TitleCrystal structure of the neutralizing Fab fragment AbD1556 bound to the BMP type I receptor IA
Components
  • Antibody fragment Fab AbD1556, heavy chain
  • Antibody fragment Fab AbD1556, light chain
  • Bone morphogenetic protein receptor type-1A
KeywordsIMMUNE SYSTEM / Antibody-antigen complex / BMP receptor extracellular domain / Bone morphogenetic protein
Function / homology
Function and homology information


neural plate mediolateral regionalization / paraxial mesoderm structural organization / positive regulation of cardiac ventricle development / fibrous ring of heart morphogenesis / positive regulation of transforming growth factor beta2 production / Mullerian duct regression / heart formation / atrioventricular node cell development / mesendoderm development / tricuspid valve morphogenesis ...neural plate mediolateral regionalization / paraxial mesoderm structural organization / positive regulation of cardiac ventricle development / fibrous ring of heart morphogenesis / positive regulation of transforming growth factor beta2 production / Mullerian duct regression / heart formation / atrioventricular node cell development / mesendoderm development / tricuspid valve morphogenesis / atrioventricular valve development / dorsal aorta morphogenesis / central nervous system neuron differentiation / cardiac right ventricle morphogenesis / BMP binding / regulation of cardiac muscle cell proliferation / hindlimb morphogenesis / negative regulation of muscle cell differentiation / negative regulation of smooth muscle cell migration / pharyngeal arch artery morphogenesis / lateral mesoderm development / regulation of lateral mesodermal cell fate specification / ventricular compact myocardium morphogenesis / pituitary gland development / mitral valve morphogenesis / BMP receptor activity / regulation of cellular senescence / dorsal/ventral axis specification / neural crest cell development / transforming growth factor beta receptor activity, type I / ectoderm development / cardiac conduction system development / endocardial cushion formation / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / cellular response to BMP stimulus / Signaling by BMP / outflow tract septum morphogenesis / ventricular trabecula myocardium morphogenesis / dorsal/ventral pattern formation / positive regulation of mesenchymal cell proliferation / endocardial cushion morphogenesis / embryonic digit morphogenesis / ventricular septum morphogenesis / roof of mouth development / odontogenesis of dentin-containing tooth / SMAD binding / outflow tract morphogenesis / positive regulation of SMAD protein signal transduction / somatic stem cell population maintenance / mesoderm formation / developmental growth / embryonic organ development / BMP signaling pathway / chondrocyte differentiation / positive regulation of bone mineralization / somitogenesis / positive regulation of osteoblast differentiation / positive regulation of cardiac muscle cell proliferation / positive regulation of vascular associated smooth muscle cell proliferation / transforming growth factor beta receptor signaling pathway / positive regulation of epithelial cell proliferation / epithelial cell proliferation / lung development / HFE-transferrin receptor complex / cellular response to growth factor stimulus / positive regulation of miRNA transcription / negative regulation of neurogenesis / osteoblast differentiation / angiogenesis / in utero embryonic development / receptor complex / immune response / external side of plasma membrane / negative regulation of gene expression / protein serine/threonine kinase activity / neuronal cell body / dendrite / positive regulation of gene expression / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor domain / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily ...GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor domain / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Ribbon / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Bone morphogenetic protein receptor type-1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMueller, T.D. / Harth, S. / Sebald, W.
CitationJournal: Plos One / Year: 2010
Title: A selection fit mechanism in BMP receptor IA as a possible source for BMP ligand-receptor promiscuity
Authors: Harth, S. / Kotzsch, A. / Hu, J. / Sebald, W. / Mueller, T.D.
History
DepositionJun 14, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 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
H: Antibody fragment Fab AbD1556, heavy chain
L: Antibody fragment Fab AbD1556, light chain
A: Bone morphogenetic protein receptor type-1A
I: Antibody fragment Fab AbD1556, heavy chain
M: Antibody fragment Fab AbD1556, light chain
B: Bone morphogenetic protein receptor type-1A
J: Antibody fragment Fab AbD1556, heavy chain
N: Antibody fragment Fab AbD1556, light chain
C: Bone morphogenetic protein receptor type-1A
K: Antibody fragment Fab AbD1556, heavy chain
O: Antibody fragment Fab AbD1556, light chain
D: Bone morphogenetic protein receptor type-1A


Theoretical massNumber of molelcules
Total (without water)247,36712
Polymers247,36712
Non-polymers00
Water48627
1
H: Antibody fragment Fab AbD1556, heavy chain
L: Antibody fragment Fab AbD1556, light chain
A: Bone morphogenetic protein receptor type-1A


Theoretical massNumber of molelcules
Total (without water)61,8423
Polymers61,8423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-25 kcal/mol
Surface area22930 Å2
MethodPISA
2
I: Antibody fragment Fab AbD1556, heavy chain
M: Antibody fragment Fab AbD1556, light chain
B: Bone morphogenetic protein receptor type-1A


Theoretical massNumber of molelcules
Total (without water)61,8423
Polymers61,8423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-26 kcal/mol
Surface area23530 Å2
MethodPISA
3
J: Antibody fragment Fab AbD1556, heavy chain
N: Antibody fragment Fab AbD1556, light chain
C: Bone morphogenetic protein receptor type-1A


Theoretical massNumber of molelcules
Total (without water)61,8423
Polymers61,8423
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-27 kcal/mol
Surface area23540 Å2
MethodPISA
4
K: Antibody fragment Fab AbD1556, heavy chain
O: Antibody fragment Fab AbD1556, light chain
D: Bone morphogenetic protein receptor type-1A


Theoretical massNumber of molelcules
Total (without water)61,8423
Polymers61,8423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-25 kcal/mol
Surface area23510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.320, 129.255, 100.239
Angle α, β, γ (deg.)90.00, 92.27, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11K
21I
31J
12O
22M
32N
42L
13D
23A
33B
43C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111K2 - 220
2111I2 - 220
3111J2 - 220
1121O2 - 213
2121M2 - 213
3121N2 - 213
4121L2 - 213
1131D34 - 117
2131A34 - 117
3131B34 - 117
4131C34 - 117

NCS ensembles :
ID
3
1
2

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Components

#1: Antibody
Antibody fragment Fab AbD1556, heavy chain


Mass: 25152.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody
Antibody fragment Fab AbD1556, light chain


Mass: 22488.762 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein
Bone morphogenetic protein receptor type-1A / BMP type I receptor / BMPR-IA / BMP type-1A receptor / BMPR-1A / Serine/threonine-protein kinase ...BMP type I receptor / BMPR-IA / BMP type-1A receptor / BMPR-1A / Serine/threonine-protein kinase receptor R5 / SKR5 / Activin receptor-like kinase 3 / ALK-3


Mass: 14199.918 Da / Num. of mol.: 4 / Fragment: extracellular domain, UNP residues 24-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMPR1A / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P36894, receptor protein serine/threonine kinase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Tris-HCl pH 7.0, 20% (w/v) PEG 8000 and 10% (w/v) glucose , VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 15, 2005 / Details: Varimax Cu HighRes
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30.4 Å / Num. all: 62444 / Num. obs: 59539 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 65.2 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 8.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 2.7 / Num. unique all: 6237 / Rsym value: 0.341 / % possible all: 97.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AQK

1aqk


Resolution: 2.7→30.4 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.879 / SU B: 30.456 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R Free: 0.408 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28044 3020 5.1 %RANDOM
Rwork0.23409 ---
obs0.23643 56514 95.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 64.104 Å2
Baniso -1Baniso -2Baniso -3
1-3.25 Å20 Å20.99 Å2
2---1.23 Å2-0 Å2
3----1.95 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15323 0 0 27 15350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02215719
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.95321442
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6552022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16924.566611
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.787152423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.561560
X-RAY DIFFRACTIONr_chiral_restr0.1140.22414
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111892
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.533210136
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.828316401
X-RAY DIFFRACTIONr_scbond_it0.62425583
X-RAY DIFFRACTIONr_scangle_it0.88235041
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11K1607tight positional0.090.05
12I1607tight positional0.060.05
13J1607tight positional0.070.05
21O1558tight positional0.090.05
22M1558tight positional0.080.05
23N1558tight positional0.110.05
24L1558tight positional0.110.05
31D647tight positional0.060.05
32A647tight positional0.060.05
33B647tight positional0.060.05
34C647tight positional0.090.05
11K1607tight thermal0.150.5
12I1607tight thermal0.140.5
13J1607tight thermal0.130.5
21O1558tight thermal0.140.5
22M1558tight thermal0.130.5
23N1558tight thermal0.120.5
24L1558tight thermal0.130.5
31D647tight thermal0.120.5
32A647tight thermal0.120.5
33B647tight thermal0.10.5
34C647tight thermal0.110.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 247 -
Rwork0.32 4254 -
obs-6101 98.04 %
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)
15.9582-1.945-1.38532.01810.67643.0161-0.15750.0545-0.3080.00230.09830.050.5116-0.13190.05920.2877-0.01340.05240.01920.00050.061229.714212.071911.7351
29.6518-3.9644-2.29254.3688-4.349711.2272-0.08490.2838-0.39-0.7515-0.7328-0.50931.46261.06140.81770.81830.42280.21540.41020.09020.768865.089412.135628.5886
37.0582-0.77271.48712.53910.58661.7146-0.1363-0.11910.20610.010.07620.14420.3451-0.07320.06010.31840.03750.0450.0496-0.01230.078529.198523.47331.1107
48.58893.6623-6.31444.4082-4.086112.0414-0.1535-0.06950.11260.10980.0585-0.5047-0.16820.34770.0950.16180.1718-0.11560.263-0.06090.300257.260527.271928.6114
54.618-1.9701-1.321512.31641.50263.4431-0.2072-0.2744-0.17651.3357-0.02991.23690.1204-0.62740.23710.2743-0.00940.12130.38480.0910.31745.289524.843420.7751
66.36231.0436-2.29072.8405-0.62842.23020.24590.61130.3765-0.2146-0.09220.0583-0.0467-0.4121-0.15380.0570.0792-0.00520.21010.02830.05393.2745-0.042540.0704
77.9486-2.3689-2.099813.6483-2.4815.55890.36770.64380.1721-0.3868-0.1797-0.53490.10070.3728-0.1880.07270.12330.05110.25440.02360.326342.0932-12.258336.1155
87.2127-0.19250.08541.2917-0.82952.45470.03390.1463-0.43840.1387-0.12050.02420.1957-0.31510.08660.1236-0.0753-0.05670.11960.00450.1416.5818-20.64548.0805
97.44465.74821.87039.4334.59224.73830.2861-0.08590.00240.1377-0.0639-0.21260.28230.1718-0.22220.12090.1133-0.05930.16380.02580.327534.3121-15.070450.7749
106.1632.73990.42997.5604-2.088812.49450.11130.4202-0.64630.58780.18990.51691.2475-1.0145-0.30110.2343-0.17070.05080.4796-0.12850.3342-18.3269-14.41853.1237
115.70441.97671.64234.40061.29112.36370.0560.2569-0.2458-0.27640.0347-0.28120.33860.0116-0.09070.3466-0.11090.04590.0677-0.04420.120444.844531.454291.6261
127.0717-1.97941.204310.53881.3625.1518-0.05090.79920.2404-0.39910.13720.4209-0.2095-0.6014-0.08630.2589-0.1072-0.07110.64420.14950.1875.666243.611986.3455
137.21510.59590.41010.15160.03982.3569-0.0892-0.05110.3045-0.11960.1083-0.0770.1993-0.009-0.01910.3507-0.10110.01310.1021-0.09440.176640.634151.8384100.1256
146.41064.31-1.73468.4982-2.56425.1503-0.13240.27680.1790.11710.28160.1017-0.1127-0.162-0.14920.13180.0695-0.07410.24670.08290.122112.828145.5453100.8181
154.942.0612-0.05784.33562.632411.47950.0617-0.15690.14440.3280.0501-0.6807-1.2140.7685-0.11180.3969-0.1216-0.07240.2298-0.0220.551865.562745.7734106.6455
165.9177-1.3626-0.13322.10950.30132.73180.31220.05260.133-0.0478-0.05520.0715-0.4374-0.1395-0.2570.12020.00970.03050.0730.00130.055621.194118.965861.4381
174.0469-0.27770.04524.4784-1.63476.38890.3495-0.09420.3730.8599-0.2190.5876-0.2001-0.6276-0.13050.27240.01280.14690.2004-0.05310.3956-16.853418.093776.6165
185.65430.2645-0.99281.6715-0.80761.54780.1978-0.213-0.28770.2501-0.156-0.23170.28120.0912-0.04180.3172-0.1253-0.09270.11230.01020.091920.03237.578780.6345
197.99351.41864.64112.68792.36367.99730.4519-0.0551-0.15430.5318-0.33250.2290.2412-0.0544-0.11940.2033-0.07450.08950.10130.01230.112-7.76973.931976.177
203.7119-3.0908-0.381319.7372-2.6057.08290.1678-1.0385-0.05431.2650.0242-1.42560.31640.9904-0.1920.1813-0.0176-0.20.6571-0.1140.308644.57645.028972.3083
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 120
2X-RAY DIFFRACTION2H121 - 221
3X-RAY DIFFRACTION3L2 - 120
4X-RAY DIFFRACTION4L121 - 211
5X-RAY DIFFRACTION5A34 - 118
6X-RAY DIFFRACTION6I1 - 120
7X-RAY DIFFRACTION7I121 - 221
8X-RAY DIFFRACTION8M2 - 120
9X-RAY DIFFRACTION9M121 - 211
10X-RAY DIFFRACTION10B34 - 118
11X-RAY DIFFRACTION11J1 - 120
12X-RAY DIFFRACTION12J121 - 221
13X-RAY DIFFRACTION13N2 - 120
14X-RAY DIFFRACTION14N121 - 211
15X-RAY DIFFRACTION15C34 - 118
16X-RAY DIFFRACTION16K1 - 120
17X-RAY DIFFRACTION17K121 - 221
18X-RAY DIFFRACTION18O2 - 120
19X-RAY DIFFRACTION19O121 - 211
20X-RAY DIFFRACTION20D34 - 118

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