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- PDB-6de7: Crystal Structure at 4.3 A Resolution of Glycosylated HIV-1 Clade... -

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Basic information

Entry
Database: PDB / ID: 6de7
TitleCrystal Structure at 4.3 A Resolution of Glycosylated HIV-1 Clade A BG505 SOSIP.664 Prefusion Env Trimer with Interdomain Stabilization 113C-429GCG in Complex with Broadly Neutralizing Antibodies PGT122 and 35O22
Components
  • (Envelope glycoprotein ...) x 2
  • 35O22 heavy chain
  • 35O22 light chain
  • PGT122 Heavy chain
  • PGT122 Light Chain
KeywordsIMMUNE SYSTEM / HIV-1 / SOSIP / Disulfide / Trimer
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / CD22 mediated BCR regulation / complement-dependent cytotoxicity / Alpha-defensins / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement ...Synthesis and processing of ENV and VPU / evasion of host immune response / CD22 mediated BCR regulation / complement-dependent cytotoxicity / Alpha-defensins / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / Dectin-2 family / immunoglobulin receptor binding / immunoglobulin mediated immune response / FCGR activation / Binding and entry of HIV virion / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / complement activation, classical pathway / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / antigen binding / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / host cell endosome membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Assembly Of The HIV Virion / Budding and maturation of HIV virion / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / Interleukin-4 and Interleukin-13 signaling / blood microparticle / Potential therapeutics for SARS / adaptive immune response / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1 / Envelope glycoprotein gp160 / Immunoglobulin lambda constant 2 / Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.123 Å
AuthorsGorman, J. / Kwong, P.D.
CitationJournal: Cell Host Microbe / Year: 2018
Title: Interdomain Stabilization Impairs CD4 Binding and Improves Immunogenicity of the HIV-1 Envelope Trimer.
Authors: Zhang, P. / Gorman, J. / Geng, H. / Liu, Q. / Lin, Y. / Tsybovsky, Y. / Go, E.P. / Dey, B. / Andine, T. / Kwon, A. / Patel, M. / Gururani, D. / Uddin, F. / Guzzo, C. / Cimbro, R. / Miao, H. ...Authors: Zhang, P. / Gorman, J. / Geng, H. / Liu, Q. / Lin, Y. / Tsybovsky, Y. / Go, E.P. / Dey, B. / Andine, T. / Kwon, A. / Patel, M. / Gururani, D. / Uddin, F. / Guzzo, C. / Cimbro, R. / Miao, H. / McKee, K. / Chuang, G.Y. / Martin, L. / Sironi, F. / Malnati, M.S. / Desaire, H. / Berger, E.A. / Mascola, J.R. / Dolan, M.A. / Kwong, P.D. / Lusso, P.
History
DepositionMay 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _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_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 24, 2021Group: Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / entity_src_gen / struct_conn
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line ..._chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Envelope glycoprotein gp160
D: 35O22 heavy chain
E: 35O22 light chain
G: Envelope glycoprotein gp160
H: PGT122 Heavy chain
L: PGT122 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,58228
Polymers169,0636
Non-polymers11,51922
Water0
1
B: Envelope glycoprotein gp160
D: 35O22 heavy chain
E: 35O22 light chain
G: Envelope glycoprotein gp160
H: PGT122 Heavy chain
L: PGT122 Light Chain
hetero molecules

B: Envelope glycoprotein gp160
D: 35O22 heavy chain
E: 35O22 light chain
G: Envelope glycoprotein gp160
H: PGT122 Heavy chain
L: PGT122 Light Chain
hetero molecules

B: Envelope glycoprotein gp160
D: 35O22 heavy chain
E: 35O22 light chain
G: Envelope glycoprotein gp160
H: PGT122 Heavy chain
L: PGT122 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)541,74584
Polymers507,19018
Non-polymers34,55666
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)128.655, 128.655, 312.918
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11G-655-

SO4

21G-655-

SO4

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Components

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Envelope glycoprotein ... , 2 types, 2 molecules BG

#1: Protein Envelope glycoprotein gp160 / Env polyprotein


Mass: 17146.482 Da / Num. of mol.: 1 / Mutation: I559P, T605C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line: HEK293 / Gene: env / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q2N0S7, UniProt: P04578*PLUS
#4: Protein Envelope glycoprotein gp160 / Env polyprotein


Mass: 54112.379 Da / Num. of mol.: 1
Mutation: D113C, T332N, R429G, A501C, E509R, K510R, A512R, V513R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6

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Protein , 2 types, 2 molecules DH

#2: Protein 35O22 heavy chain


Mass: 26170.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK293 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01857*PLUS
#5: Protein PGT122 Heavy chain


Mass: 25434.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01857*PLUS

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Antibody , 2 types, 2 molecules EL

#3: Antibody 35O22 light chain


Mass: 23318.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#6: Antibody PGT122 Light Chain


Mass: 22880.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0DOY2*PLUS

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Sugars , 8 types, 21 molecules

#7: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#9: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#10: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#11: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#12: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#13: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#14: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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

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Non-polymers , 1 types, 1 molecules

#15: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 4.42 Å3/Da / Density % sol: 72.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 24%PEG400, 3% PEG3350, 0.1M sodium acetate 5.5, 0.2M LiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.16
ReflectionResolution: 4.1→50 Å / Num. obs: 16811 / % possible obs: 75.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.064 / Rrim(I) all: 0.193 / Χ2: 0.941 / Net I/σ(I): 7.4 / Num. measured all: 111641
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4.1-4.23.40.7266340.7330.3170.8011.07844
4.2-4.33.60.5286700.9410.2270.5811.13945.7
4.3-4.423.70.4397440.8130.1860.4811.06549.8
4.42-4.553.90.487260.8380.2040.5270.96249
4.55-4.693.80.4198430.8770.1790.461.0357.3
4.69-4.8640.399290.8830.1620.4261.06662.4
4.86-5.054.20.3869870.90.1590.420.9167.6
5.05-5.284.60.39911560.9320.1650.4351.03276.2
5.28-5.565.10.37612490.9270.150.4080.93584.9
5.56-5.916.30.53513960.8860.2080.5770.89295.5
5.91-6.378.40.55415100.9290.1960.5890.881100
6.37-7.019.60.47314860.950.1580.4990.886100
7.01-8.029.80.25814830.9810.0840.2710.881100
8.02-10.099.70.13114890.9910.0420.1380.896100
10.09-509.30.12115090.9680.0410.1291.05899.1

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Processing

Software
NameVersionClassification
PHENIX(dev_3126: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TVP

4tvp


Resolution: 4.123→42.112 Å / Cross valid method: THROUGHOUT / σ(F): 171.55 / Phase error: 30.57 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.258 1442 5.7 %
Rwork0.2485 --
obs0.252 14134 56.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.123→42.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10942 0 762 0 11704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412045
X-RAY DIFFRACTIONf_angle_d0.74616512
X-RAY DIFFRACTIONf_dihedral_angle_d10.9967142
X-RAY DIFFRACTIONf_chiral_restr0.0482020
X-RAY DIFFRACTIONf_plane_restr0.0041993
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1402-4.30570.3179380.2839703X-RAY DIFFRACTION14
4.3057-4.50130.2677480.2392972X-RAY DIFFRACTION20
4.5013-4.73820.304680.24971254X-RAY DIFFRACTION25
4.7382-5.03430.2168790.23951620X-RAY DIFFRACTION34
5.0343-5.42190.23741180.25722233X-RAY DIFFRACTION45
5.4219-5.96550.25481810.27993405X-RAY DIFFRACTION70
5.9655-6.82390.33762460.2924474X-RAY DIFFRACTION91
6.8239-8.57920.24342530.2564666X-RAY DIFFRACTION95
8.5792-36.71060.2362480.22024626X-RAY DIFFRACTION95
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)
10.52990.5585-0.8750.7176-1.04461.56180.0564-0.2448-0.04520.1957-0.0298-0.07590.01810.1541-0.02030.8678-0.11180.26430.9580.15680.15651.616652.5809187.2896
20.590.24690.02130.8609-0.10630.018-0.19130.26740.0106-0.17620.0633-0.0326-0.1474-0.23270.1241.8925-0.1732-0.30911.29370.04581.21446.995767.3796162.0764
32.0040.7770.39751.7763-0.98591.50250.0238-0.1486-0.2438-0.12250.2430.01220.40170.1288-0.13820.8126-0.00440.07610.51280.13090.0762-3.655568.1487176.5991
40.3902-0.13350.53631.3178-0.77441.0223-0.1665-0.01940.0750.3316-0.17250.1597-0.2806-0.520.03231.0280.1510.51761.040.06410.3677-14.84762.3462195.0673
51.2182-0.21240.14740.86360.38190.21690.0067-0.0175-0.38350.3350.0670.14810.0249-0.1658-0.01861.84670.09950.46141.19290.18470.665-10.831722.4468194.1254
60.5372-0.0795-0.11130.66-0.09180.2133-0.14220.20070.13450.2255-0.17290.05090.0605-0.2970.29661.9338-0.41330.13691.9483-0.17491.63-35.39537.3476191.736
70.04370.0103-0.20131.0619-0.1010.98170.0261-0.9828-0.00460.8191-0.01780.57390.14840.2716-0.01771.9072-0.07280.59261.6260.01010.7989-19.115631.5559213.1001
80.6908-0.2996-0.25710.55260.87711.4787-0.07190.1763-0.05050.3943-0.07490.22490.3466-0.2290.14452.1505-0.28070.26911.72370.29251.9353-44.88853.5065205.7414
91.8223-0.2290.48371.97850.66311.2995-0.21150.69750.273-0.46250.1824-0.7060.22170.36780.04991.13220.15650.26790.75650.05940.51543.378355.3684171.4185
100.2024-0.26230.05120.4039-0.01850.7338-0.10870.4273-0.3578-0.14110.04760.22210.1026-0.04030.1551.2770.03390.57750.9325-0.13710.07231.121148.8133143.2793
110.7714-0.1602-0.690.21760.32882.6062-0.23920.1036-0.3984-0.2179-0.1620.31090.9184-0.43040.31271.2798-0.11920.37650.9022-0.12420.2377-0.109940.7472146.6065
120.0787-0.1563-0.21780.33870.43740.65550.08460.1358-0.3665-0.09030.12980.12560.4948-0.14410.00721.67660.10450.38661.6592-0.48060.623819.936720.084998.9423
131.20310.5670.15290.43570.00720.05740.35230.0688-0.1628-0.61630.2584-0.4822-0.16150.1183-0.56971.84260.24170.55151.4798-0.21431.063743.916613.869877.4239
140.76830.08870.09150.7506-0.21410.1220.08230.19560.00520.0296-0.008-0.53010.0380.0674-0.07971.54890.08940.2861.2769-0.30380.686535.937831.4624109.4433
150.75870.18210.44490.70790.29470.31130.357-0.10510.36240.04450.1336-0.0182-0.08040.0854-0.46551.4908-0.25440.40351.5043-0.20240.901551.580828.566173.6909
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 518 through 544 )
2X-RAY DIFFRACTION2chain 'B' and (resid 545 through 570 )
3X-RAY DIFFRACTION3chain 'B' and (resid 571 through 600 )
4X-RAY DIFFRACTION4chain 'B' and (resid 601 through 664 )
5X-RAY DIFFRACTION5chain 'D' and (resid 1 through 109 )
6X-RAY DIFFRACTION6chain 'D' and (resid 110 through 211 )
7X-RAY DIFFRACTION7chain 'E' and (resid 2 through 106A )
8X-RAY DIFFRACTION8chain 'E' and (resid 107 through 210 )
9X-RAY DIFFRACTION9chain 'G' and (resid 32 through 90 )
10X-RAY DIFFRACTION10chain 'G' and (resid 91 through 298 )
11X-RAY DIFFRACTION11chain 'G' and (resid 299 through 505 )
12X-RAY DIFFRACTION12chain 'H' and (resid 1 through 118 )
13X-RAY DIFFRACTION13chain 'H' and (resid 119 through 211 )
14X-RAY DIFFRACTION14chain 'L' and (resid 8 through 114 )
15X-RAY DIFFRACTION15chain 'L' and (resid 115 through 210 )

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