[English] 日本語
Yorodumi
- PDB-3lzf: Crystal Structure of Fab 2D1 in Complex with the 1918 Influenza V... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lzf
TitleCrystal Structure of Fab 2D1 in Complex with the 1918 Influenza Virus Hemagglutinin
Components
  • (Hemagglutinin, ...) x 2
  • 2D1 Fab, Heavy Chain
  • 2D1 Fab, Light Chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / hemagglutinin / Fab / neutralizing antibodies / antibody / pandemic flu / swine flu / Envelope protein / Fusion protein / Glycoprotein / antigen / Virion / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 / membrane
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsEkiert, D.C. / Wilson, I.A.
CitationJournal: Science / Year: 2010
Title: Structural basis of preexisting immunity to the 2009 H1N1 pandemic influenza virus.
Authors: Xu, R. / Ekiert, D.C. / Krause, J.C. / Hai, R. / Crowe, J.E. / Wilson, I.A.
History
DepositionMar 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin, HA1 Subunit
B: Hemagglutinin, HA2 Subunit
H: 2D1 Fab, Heavy Chain
L: 2D1 Fab, Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1788
Polymers104,3594
Non-polymers1,8194
Water00
1
A: Hemagglutinin, HA1 Subunit
B: Hemagglutinin, HA2 Subunit
H: 2D1 Fab, Heavy Chain
L: 2D1 Fab, Light Chain
hetero molecules

A: Hemagglutinin, HA1 Subunit
B: Hemagglutinin, HA2 Subunit
H: 2D1 Fab, Heavy Chain
L: 2D1 Fab, Light Chain
hetero molecules

A: Hemagglutinin, HA1 Subunit
B: Hemagglutinin, HA2 Subunit
H: 2D1 Fab, Heavy Chain
L: 2D1 Fab, Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,53424
Polymers313,07812
Non-polymers5,45612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
2
A: Hemagglutinin, HA1 Subunit
B: Hemagglutinin, HA2 Subunit
hetero molecules

A: Hemagglutinin, HA1 Subunit
B: Hemagglutinin, HA2 Subunit
hetero molecules

A: Hemagglutinin, HA1 Subunit
B: Hemagglutinin, HA2 Subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,99818
Polymers170,5426
Non-polymers5,45612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area28120 Å2
ΔGint-147 kcal/mol
Surface area60120 Å2
MethodPISA
3
H: 2D1 Fab, Heavy Chain
L: 2D1 Fab, Light Chain


Theoretical massNumber of molelcules
Total (without water)47,5122
Polymers47,5122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-25 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.745, 161.745, 143.473
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

-
Components

-
Hemagglutinin, ... , 2 types, 2 molecules AB

#1: Protein Hemagglutinin, HA1 Subunit / Hemagglutinin HA1 chain / Hemagglutinin HA2 chain


Mass: 36452.797 Da / Num. of mol.: 1 / Fragment: Ectodomain HA1, residues 18-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/South Carolina/1/1918(H1N1) / Gene: HA, Hemagglutinin / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): BTI-TN-5B1-4 / References: UniProt: Q9WFX3
#2: Protein Hemagglutinin, HA2 Subunit / Hemagglutinin HA1 chain / Hemagglutinin HA2 chain


Mass: 20394.445 Da / Num. of mol.: 1 / Fragment: Ectodomain HA2, residues 345-520
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/South Carolina/1/1918(H1N1) / Gene: HA, Hemagglutinin / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): BTI-TN-5B1-4 / References: UniProt: Q9WFX3

-
Antibody , 2 types, 2 molecules HL

#3: Antibody 2D1 Fab, Heavy Chain


Mass: 24699.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Immunoglobulin, Gamma Chain / Plasmid: pEE6.4 / Cell line (production host): HEK 293F / Organ (production host): kidney / Production host: Homo sapiens (human)
#4: Antibody 2D1 Fab, Light Chain


Mass: 22812.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Immunoglobulin, Lambda Chain / Plasmid: pEE12.4 / Cell line (production host): HEK 293F / Organ (production host): kidney / Production host: Homo sapiens (human)

-
Sugars , 3 types, 4 molecules

#5: 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.: 2
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
#6: 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
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.19 Å3/Da / Density % sol: 76.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 16% PEG1000, 100mM PIPES pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0333 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 54245 / Num. obs: 53366 / % possible obs: 98.4 % / Observed criterion σ(I): 1 / Redundancy: 10.3 % / Biso Wilson estimate: 90.4 Å2 / Rsym value: 0.04
Reflection shellResolution: 2.8→2.89 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.49

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.4.0069refinement
HKL-2000data reduction
XPREPdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49.69 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.919 / SU B: 28.678 / SU ML: 0.251 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 2596 4.9 %RANDOM
Rwork0.2301 ---
obs0.23154 50122 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.287 Å2
Baniso -1Baniso -2Baniso -3
1-2.96 Å21.48 Å20 Å2
2--2.96 Å20 Å2
3----4.44 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7087 0 120 0 7207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227401
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.96710097
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.855921
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64524.801302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.626151160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3911526
X-RAY DIFFRACTIONr_chiral_restr0.1080.21150
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215560
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_it0.6291.54597
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21927434
X-RAY DIFFRACTIONr_scbond_it1.99232804
X-RAY DIFFRACTIONr_scangle_it3.3844.52662
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 189 -
Rwork0.414 3230 -
obs--87.46 %
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)
12.10810.6513-3.39931.1235-1.91377.15370.1842-0.07620.0502-0.1275-0.3008-0.0084-0.30380.32710.1166-0.498-0.12070.0344-0.36760.0579-0.278661.0598-41.261646.3841
22.0350.42523.06251.44880.092212.23890.0950.9820.2094-1.18470.07780.43020.3235-0.6564-0.17290.51120.1052-0.26470.50420.1551-0.296768.7448-44.1739-6.4675
36.21354.3923-4.29676.0701-4.8837.32861.2646-1.9979-0.65021.8344-1.4953-0.528-1.03081.3520.2307-0.0812-0.554-0.23350.48170.2715-0.235341.096-62.8934100.1929
42.27183.2345-1.97818.2461-6.02319.96480.2035-1.5609-1.8410.3829-1.4413-1.78971.53361.11531.2377-0.1105-0.0982-0.16360.71660.9970.793247.7756-79.490297.3284
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 325
2X-RAY DIFFRACTION2B1 - 173
3X-RAY DIFFRACTION3H2 - 223
4X-RAY DIFFRACTION4L2 - 211

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more